Diff of the two buildlogs:

--
--- b1/build.log	2023-06-12 21:41:40.043550071 +0000
+++ b2/build.log	2023-06-12 21:43:00.728016736 +0000
@@ -1,8 +1,2509 @@
+W: cgroups are not available on the host, not using them.
 I: pbuilder: network access will be disabled during build
-I: Current time: Mon Jun 12 09:38:51 -12 2023
-I: pbuilder-time-stamp: 1686605931
+I: Current time: Mon Jul 15 18:04:41 +14 2024
+I: pbuilder-time-stamp: 1721016281
 I: Building the build Environment
 I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz]
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+/usr/bin/tar: ./usr/lib/locale/en_IE.utf8: time stamp 2025-08-15 13:11:25 is 34196797.085708353 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CR/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.085671947 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CR: time stamp 2025-08-15 13:11:25 is 34196797.085638189 s in the future
+/usr/bin/tar: ./usr/lib/locale/he_IL.utf8: time stamp 2025-08-15 13:11:25 is 34196797.085605226 s in the future
+/usr/bin/tar: ./usr/lib/locale/om_ET: time stamp 2025-08-15 13:11:25 is 34196797.085572353 s in the future
+/usr/bin/tar: ./usr/lib/locale/en_NZ/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.085539399 s in the future
+/usr/bin/tar: ./usr/lib/locale/en_NZ: time stamp 2025-08-15 13:11:25 is 34196797.085505681 s in the future
+/usr/bin/tar: ./usr/lib/locale/nn_NO/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.085472074 s in the future
+/usr/bin/tar: ./usr/lib/locale/nn_NO: time stamp 2025-08-15 13:11:25 is 34196797.085438297 s in the future
+/usr/bin/tar: ./usr/lib/locale/nhn_MX: time stamp 2025-08-15 13:11:25 is 34196797.085404858 s in the future
+/usr/bin/tar: ./usr/lib/locale/sl_SI.utf8: time stamp 2025-08-15 13:11:25 is 34196797.085371141 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CL/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.085337286 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CL: time stamp 2025-08-15 13:11:25 is 34196797.085303712 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CO.utf8/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.08527124 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CO.utf8: time stamp 2025-08-15 13:11:25 is 34196797.085239061 s in the future
+/usr/bin/tar: ./usr/lib/locale/ast_ES: time stamp 2025-08-15 13:11:25 is 34196797.085205332 s in the future
+/usr/bin/tar: ./usr/lib/locale/fa_IR: time stamp 2025-08-15 13:11:25 is 34196797.085172069 s in the future
+/usr/bin/tar: ./usr/lib/locale/mhr_RU: time stamp 2025-08-15 13:11:25 is 34196797.085140319 s in the future
+/usr/bin/tar: ./usr/lib/locale/ar_YE/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.085107023 s in the future
+/usr/bin/tar: ./usr/lib/locale/ar_YE: time stamp 2025-08-15 13:11:25 is 34196797.085074662 s in the future
+/usr/bin/tar: ./usr/lib/locale/it_CH: time stamp 2025-08-15 13:11:25 is 34196797.085040834 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_MX.utf8/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.085008799 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_MX.utf8: time stamp 2025-08-15 13:11:25 is 34196797.084974462 s in the future
+/usr/bin/tar: ./usr/lib/locale/en_PH.utf8/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.084941714 s in the future
+/usr/bin/tar: ./usr/lib/locale/en_PH.utf8: time stamp 2025-08-15 13:11:25 is 34196797.084907465 s in the future
+/usr/bin/tar: ./usr/lib/locale/sv_SE/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.084874278 s in the future
+/usr/bin/tar: ./usr/lib/locale/sv_SE: time stamp 2025-08-15 13:11:25 is 34196797.084840887 s in the future
+/usr/bin/tar: ./usr/lib/locale/sw_KE: time stamp 2025-08-15 13:11:25 is 34196797.084808335 s in the future
+/usr/bin/tar: ./usr/lib/locale/shs_CA/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.084774655 s in the future
+/usr/bin/tar: ./usr/lib/locale/shs_CA: time stamp 2025-08-15 13:11:25 is 34196797.084741925 s in the future
+/usr/bin/tar: ./usr/lib/locale/nl_NL@euro/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.084707953 s in the future
+/usr/bin/tar: ./usr/lib/locale/nl_NL@euro: time stamp 2025-08-15 13:11:25 is 34196797.084675321 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CR.utf8/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.084641672 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CR.utf8: time stamp 2025-08-15 13:11:25 is 34196797.084605184 s in the future
+/usr/bin/tar: ./usr/lib/locale/gez_ER/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.084571861 s in the future
+/usr/bin/tar: ./usr/lib/locale/gez_ER: time stamp 2025-08-15 13:11:25 is 34196797.084539998 s in the future
+/usr/bin/tar: ./usr/lib/locale/ga_IE: time stamp 2025-08-15 13:11:25 is 34196797.084506491 s in the future
+/usr/bin/tar: ./usr/lib/locale/tl_PH: time stamp 2025-08-15 13:11:25 is 34196797.084474431 s in the future
+/usr/bin/tar: ./usr/lib/locale/bn_BD: time stamp 2025-08-15 13:11:25 is 34196797.084438387 s in the future
+/usr/bin/tar: ./usr/lib/locale/ks_IN: time stamp 2025-08-15 13:11:25 is 34196797.084404032 s in the future
+/usr/bin/tar: ./usr/lib/locale/lij_IT: time stamp 2025-08-15 13:11:25 is 34196797.084370761 s in the future
+/usr/bin/tar: ./usr/lib/locale/sv_FI.utf8: time stamp 2025-08-15 13:11:25 is 34196797.08433587 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_ES/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.084303114 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_ES: time stamp 2025-08-15 13:11:25 is 34196797.084268794 s in the future
+/usr/bin/tar: ./usr/lib/locale/en_IE@euro/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.08423577 s in the future
+/usr/bin/tar: ./usr/lib/locale/en_IE@euro: time stamp 2025-08-15 13:11:25 is 34196797.08420195 s in the future
+/usr/bin/tar: ./usr/lib/locale/mai_IN/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.084168921 s in the future
+/usr/bin/tar: ./usr/lib/locale/mai_IN: time stamp 2025-08-15 13:11:25 is 34196797.084136329 s in the future
+/usr/bin/tar: ./usr/lib/locale/ia_FR: time stamp 2025-08-15 13:11:25 is 34196797.084104885 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_UY/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.084072814 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_UY: time stamp 2025-08-15 13:11:25 is 34196797.084040226 s in the future
+/usr/bin/tar: ./usr/lib/locale/cs_CZ.utf8: time stamp 2025-08-15 13:11:25 is 34196797.08400728 s in the future
+/usr/bin/tar: ./usr/lib/locale/pt_PT/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.08397455 s in the future
+/usr/bin/tar: ./usr/lib/locale/pt_PT: time stamp 2025-08-15 13:11:25 is 34196797.083941249 s in the future
+/usr/bin/tar: ./usr/lib/locale/crh_UA: time stamp 2025-08-15 13:11:25 is 34196797.083907773 s in the future
+/usr/bin/tar: ./usr/lib/locale/tr_CY: time stamp 2025-08-15 13:11:25 is 34196797.08387344 s in the future
+/usr/bin/tar: ./usr/lib/locale/mr_IN: time stamp 2025-08-15 13:11:25 is 34196797.083840334 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CO/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.083806859 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CO: time stamp 2025-08-15 13:11:25 is 34196797.083755612 s in the future
+/usr/bin/tar: ./usr/lib/locale/so_DJ: time stamp 2025-08-15 13:11:25 is 34196797.083720692 s in the future
+/usr/bin/tar: ./usr/lib/locale/de_DE@euro/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.083687147 s in the future
+/usr/bin/tar: ./usr/lib/locale/de_DE@euro: time stamp 2025-08-15 13:11:25 is 34196797.083654165 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CL.utf8/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.083621808 s in the future
+/usr/bin/tar: ./usr/lib/locale/es_CL.utf8: time stamp 2025-08-15 13:11:25 is 34196797.083587972 s in the future
+/usr/bin/tar: ./usr/lib/locale/li_BE/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.083555141 s in the future
+/usr/bin/tar: ./usr/lib/locale/li_BE: time stamp 2025-08-15 13:11:25 is 34196797.083516579 s in the future
+/usr/bin/tar: ./usr/lib/locale/fil_PH: time stamp 2025-08-15 13:11:25 is 34196797.083483383 s in the future
+/usr/bin/tar: ./usr/lib/locale/is_IS: time stamp 2025-08-15 13:11:25 is 34196797.083449591 s in the future
+/usr/bin/tar: ./usr/lib/locale/ca_FR/LC_MESSAGES: time stamp 2025-08-15 13:11:25 is 34196797.083417103 s in the future
+/usr/bin/tar: ./usr/lib/locale/ca_FR: time stamp 2025-08-15 13:11:25 is 34196797.083383345 s in the future
+/usr/bin/tar: ./usr/lib/locale/gd_GB: time stamp 2025-08-15 13:11:25 is 34196797.083350471 s in the future
+/usr/bin/tar: ./usr/lib/locale/lt_LT.utf8: time stamp 2025-08-15 13:11:25 is 34196797.083315809 s in the future
+/usr/bin/tar: ./usr/lib/locale: time stamp 2025-08-15 13:11:25 is 34196797.083283222 s in the future
+/usr/bin/tar: ./usr/lib/gold-ld: time stamp 2025-08-15 13:11:13 is 34196785.083250737 s in the future
+/usr/bin/tar: ./usr/lib/bfd-plugins: time stamp 2025-08-15 13:11:18 is 34196790.083217365 s in the future
+/usr/bin/tar: ./usr/lib/i386-linux-gnu/perl/cross-config-5.36.0: time stamp 2025-08-15 13:11:07 is 34196779.083181991 s in the future
+/usr/bin/tar: ./usr/lib/i386-linux-gnu/perl: time stamp 2025-08-15 13:10:59 is 34196771.083148433 s in the future
+/usr/bin/tar: ./usr/lib/i386-linux-gnu: time stamp 2025-08-15 13:11:23 is 34196795.083115399 s in the future
+/usr/bin/tar: ./usr/lib/compat-ld: time stamp 2025-08-15 13:11:13 is 34196785.08308331 s in the future
+/usr/bin/tar: ./usr/lib: time stamp 2025-08-15 13:11:18 is 34196790.083050906 s in the future
+/usr/bin/tar: ./usr: time stamp 2025-08-15 13:11:01 is 34196773.083018381 s in the future
+/usr/bin/tar: ./lib: time stamp 2025-08-15 13:11:20 is 34196792.082963409 s in the future
+/usr/bin/tar: ./etc/rc6.d: time stamp 2025-08-15 13:11:11 is 34196783.082931015 s in the future
+/usr/bin/tar: ./etc/systemd/system/multi-user.target.wants: time stamp 2025-08-15 13:11:11 is 34196783.082898622 s in the future
+/usr/bin/tar: ./etc/systemd/system/timers.target.wants: time stamp 2025-08-15 13:11:12 is 34196784.082865941 s in the future
+/usr/bin/tar: ./etc/systemd/system: time stamp 2025-08-15 13:11:11 is 34196783.082832714 s in the future
+/usr/bin/tar: ./etc/alternatives: time stamp 2025-08-15 13:11:25 is 34196797.082777964 s in the future
+/usr/bin/tar: ./etc/rc0.d: time stamp 2025-08-15 13:11:11 is 34196783.08274176 s in the future
+/usr/bin/tar: ./etc/rcS.d: time stamp 2025-08-15 13:11:11 is 34196783.082707809 s in the future
+/usr/bin/tar: ./bin: time stamp 2025-08-15 13:11:23 is 34196795.082631356 s in the future
 I: copying local configuration
 W: --override-config is not set; not updating apt.conf Read the manpage for details.
 I: mounting /proc filesystem
@@ -17,7 +2518,7 @@
 I: copying [./clustalx_2.1+lgpl.orig.tar.gz]
 I: copying [./clustalx_2.1+lgpl-9.debian.tar.xz]
 I: Extracting source
-gpgv: Signature made Fri Dec  4 10:20:42 2020 -12
+gpgv: Signature made Sat Dec  5 12:20:42 2020 +14
 gpgv:                using RSA key F1F007320A035541F0A663CA578A0494D1C646D1
 gpgv:                issuer "tille@debian.org"
 gpgv: Can't check signature: No public key
@@ -31,137 +2532,168 @@
 dpkg-source: info: applying qt5.patch
 I: Not using root during the build.
 I: Installing the build-deps
-I: user script /srv/workspace/pbuilder/26567/tmp/hooks/D02_print_environment starting
+I: user script /srv/workspace/pbuilder/93232/tmp/hooks/D01_modify_environment starting
+debug: Running on ionos6-i386.
+I: Changing host+domainname to test build reproducibility
+I: Adding a custom variable just for the fun of it...
+I: Changing /bin/sh to bash
+'/bin/sh' -> '/bin/bash'
+lrwxrwxrwx 1 root root 9 Jul 15 18:04 /bin/sh -> /bin/bash
+I: Setting pbuilder2's login shell to /bin/bash
+I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other
+I: user script /srv/workspace/pbuilder/93232/tmp/hooks/D01_modify_environment finished
+I: user script /srv/workspace/pbuilder/93232/tmp/hooks/D02_print_environment starting
 I: set
-  BUILDDIR='/build'
-  BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other'
-  BUILDUSERNAME='pbuilder1'
-  BUILD_ARCH='i386'
-  DEBIAN_FRONTEND='noninteractive'
-  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 '
-  DISTRIBUTION='bookworm'
-  HOME='/root'
-  HOST_ARCH='i386'
+  BASH=/bin/sh
+  BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath
+  BASH_ALIASES=()
+  BASH_ARGC=()
+  BASH_ARGV=()
+  BASH_CMDS=()
+  BASH_LINENO=([0]="12" [1]="0")
+  BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:.
+  BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment")
+  BASH_VERSINFO=([0]="5" [1]="2" [2]="15" [3]="1" [4]="release" [5]="i686-pc-linux-gnu")
+  BASH_VERSION='5.2.15(1)-release'
+  BUILDDIR=/build
+  BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other'
+  BUILDUSERNAME=pbuilder2
+  BUILD_ARCH=i386
+  DEBIAN_FRONTEND=noninteractive
+  DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=15 '
+  DIRSTACK=()
+  DISTRIBUTION=bookworm
+  EUID=0
+  FUNCNAME=([0]="Echo" [1]="main")
+  GROUPS=()
+  HOME=/root
+  HOSTNAME=i-capture-the-hostname
+  HOSTTYPE=i686
+  HOST_ARCH=i386
   IFS=' 	
   '
-  INVOCATION_ID='d490c8d750084e4c8c705d1ecc098fad'
-  LANG='C'
-  LANGUAGE='en_US:en'
-  LC_ALL='C'
-  LD_LIBRARY_PATH='/usr/lib/libeatmydata'
-  LD_PRELOAD='libeatmydata.so'
-  MAIL='/var/mail/root'
-  OPTIND='1'
-  PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games'
-  PBCURRENTCOMMANDLINEOPERATION='build'
-  PBUILDER_OPERATION='build'
-  PBUILDER_PKGDATADIR='/usr/share/pbuilder'
-  PBUILDER_PKGLIBDIR='/usr/lib/pbuilder'
-  PBUILDER_SYSCONFDIR='/etc'
-  PPID='26567'
-  PS1='# '
-  PS2='> '
+  LANG=C
+  LANGUAGE=de_CH:de
+  LC_ALL=C
+  LD_LIBRARY_PATH=/usr/lib/libeatmydata
+  LD_PRELOAD=libeatmydata.so
+  MACHTYPE=i686-pc-linux-gnu
+  MAIL=/var/mail/root
+  OPTERR=1
+  OPTIND=1
+  OSTYPE=linux-gnu
+  PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path
+  PBCURRENTCOMMANDLINEOPERATION=build
+  PBUILDER_OPERATION=build
+  PBUILDER_PKGDATADIR=/usr/share/pbuilder
+  PBUILDER_PKGLIBDIR=/usr/lib/pbuilder
+  PBUILDER_SYSCONFDIR=/etc
+  PIPESTATUS=([0]="0")
+  POSIXLY_CORRECT=y
+  PPID=93232
   PS4='+ '
-  PWD='/'
-  SHELL='/bin/bash'
-  SHLVL='2'
-  SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0sh0fE9f/pbuilderrc_jZMO --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0sh0fE9f/b1 --logfile b1/build.log clustalx_2.1+lgpl-9.dsc'
-  SUDO_GID='112'
-  SUDO_UID='107'
-  SUDO_USER='jenkins'
-  TERM='unknown'
-  TZ='/usr/share/zoneinfo/Etc/GMT+12'
-  USER='root'
-  _='/usr/bin/systemd-run'
-  http_proxy='http://78.137.99.97:3128'
+  PWD=/
+  SHELL=/bin/bash
+  SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix
+  SHLVL=3
+  SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.0sh0fE9f/pbuilderrc_awmn --distribution bookworm --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.0sh0fE9f/b2 --logfile b2/build.log --extrapackages usrmerge clustalx_2.1+lgpl-9.dsc'
+  SUDO_GID=112
+  SUDO_UID=107
+  SUDO_USER=jenkins
+  TERM=unknown
+  TZ=/usr/share/zoneinfo/Etc/GMT-14
+  UID=0
+  USER=root
+  _='I: set'
+  http_proxy=http://85.184.249.68:3128
 I: uname -a
-  Linux ionos2-i386 6.1.0-9-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.27-1 (2023-05-08) i686 GNU/Linux
+  Linux i-capture-the-hostname 6.1.0-9-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.27-1 (2023-05-08) x86_64 GNU/Linux
 I: ls -l /bin
   total 6036
-  -rwxr-xr-x 1 root root 1408088 Apr 23 09:24 bash
-  -rwxr-xr-x 3 root root   38404 Sep 18  2022 bunzip2
-  -rwxr-xr-x 3 root root   38404 Sep 18  2022 bzcat
-  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzcmp -> bzdiff
-  -rwxr-xr-x 1 root root    2225 Sep 18  2022 bzdiff
-  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzegrep -> bzgrep
-  -rwxr-xr-x 1 root root    4893 Nov 27  2021 bzexe
-  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzfgrep -> bzgrep
-  -rwxr-xr-x 1 root root    3775 Sep 18  2022 bzgrep
-  -rwxr-xr-x 3 root root   38404 Sep 18  2022 bzip2
-  -rwxr-xr-x 1 root root   17892 Sep 18  2022 bzip2recover
-  lrwxrwxrwx 1 root root       6 Sep 18  2022 bzless -> bzmore
-  -rwxr-xr-x 1 root root    1297 Sep 18  2022 bzmore
-  -rwxr-xr-x 1 root root   42920 Sep 20  2022 cat
-  -rwxr-xr-x 1 root root   79816 Sep 20  2022 chgrp
-  -rwxr-xr-x 1 root root   67496 Sep 20  2022 chmod
-  -rwxr-xr-x 1 root root   79816 Sep 20  2022 chown
-  -rwxr-xr-x 1 root root  162024 Sep 20  2022 cp
-  -rwxr-xr-x 1 root root  136916 Jan  5 01:20 dash
-  -rwxr-xr-x 1 root root  137160 Sep 20  2022 date
-  -rwxr-xr-x 1 root root  100364 Sep 20  2022 dd
-  -rwxr-xr-x 1 root root  108940 Sep 20  2022 df
-  -rwxr-xr-x 1 root root  162152 Sep 20  2022 dir
-  -rwxr-xr-x 1 root root   87760 Mar 22 22:20 dmesg
-  lrwxrwxrwx 1 root root       8 Dec 19 01:33 dnsdomainname -> hostname
-  lrwxrwxrwx 1 root root       8 Dec 19 01:33 domainname -> hostname
-  -rwxr-xr-x 1 root root   38760 Sep 20  2022 echo
-  -rwxr-xr-x 1 root root      41 Jan 24 02:43 egrep
-  -rwxr-xr-x 1 root root   34664 Sep 20  2022 false
-  -rwxr-xr-x 1 root root      41 Jan 24 02:43 fgrep
-  -rwxr-xr-x 1 root root   84272 Mar 22 22:20 findmnt
-  -rwsr-xr-x 1 root root   30240 Mar 22 20:38 fusermount
-  -rwxr-xr-x 1 root root  218680 Jan 24 02:43 grep
-  -rwxr-xr-x 2 root root    2346 Apr  9  2022 gunzip
-  -rwxr-xr-x 1 root root    6447 Apr  9  2022 gzexe
-  -rwxr-xr-x 1 root root  100952 Apr  9  2022 gzip
-  -rwxr-xr-x 1 root root   21916 Dec 19 01:33 hostname
-  -rwxr-xr-x 1 root root   75756 Sep 20  2022 ln
-  -rwxr-xr-x 1 root root   55600 Mar 22 23:43 login
-  -rwxr-xr-x 1 root root  162152 Sep 20  2022 ls
-  -rwxr-xr-x 1 root root  214568 Mar 22 22:20 lsblk
-  -rwxr-xr-x 1 root root   96328 Sep 20  2022 mkdir
-  -rwxr-xr-x 1 root root   84008 Sep 20  2022 mknod
-  -rwxr-xr-x 1 root root   38792 Sep 20  2022 mktemp
-  -rwxr-xr-x 1 root root   63016 Mar 22 22:20 more
-  -rwsr-xr-x 1 root root   58912 Mar 22 22:20 mount
-  -rwxr-xr-x 1 root root   13856 Mar 22 22:20 mountpoint
-  -rwxr-xr-x 1 root root  157932 Sep 20  2022 mv
-  lrwxrwxrwx 1 root root       8 Dec 19 01:33 nisdomainname -> hostname
-  lrwxrwxrwx 1 root root      14 Apr  2 18:25 pidof -> /sbin/killall5
-  -rwxr-xr-x 1 root root   38792 Sep 20  2022 pwd
-  lrwxrwxrwx 1 root root       4 Apr 23 09:24 rbash -> bash
-  -rwxr-xr-x 1 root root   51080 Sep 20  2022 readlink
-  -rwxr-xr-x 1 root root   75720 Sep 20  2022 rm
-  -rwxr-xr-x 1 root root   51080 Sep 20  2022 rmdir
-  -rwxr-xr-x 1 root root   22308 Nov  2  2022 run-parts
-  -rwxr-xr-x 1 root root  133224 Jan  5 07:55 sed
-  lrwxrwxrwx 1 root root       4 Jan  5 01:20 sh -> dash
-  -rwxr-xr-x 1 root root   38760 Sep 20  2022 sleep
-  -rwxr-xr-x 1 root root   87976 Sep 20  2022 stty
-  -rwsr-xr-x 1 root root   83492 Mar 22 22:20 su
-  -rwxr-xr-x 1 root root   38792 Sep 20  2022 sync
-  -rwxr-xr-x 1 root root  598456 Apr  6 02:25 tar
-  -rwxr-xr-x 1 root root   13860 Nov  2  2022 tempfile
-  -rwxr-xr-x 1 root root  120776 Sep 20  2022 touch
-  -rwxr-xr-x 1 root root   34664 Sep 20  2022 true
-  -rwxr-xr-x 1 root root   17892 Mar 22 20:38 ulockmgr_server
-  -rwsr-xr-x 1 root root   30236 Mar 22 22:20 umount
-  -rwxr-xr-x 1 root root   38760 Sep 20  2022 uname
-  -rwxr-xr-x 2 root root    2346 Apr  9  2022 uncompress
-  -rwxr-xr-x 1 root root  162152 Sep 20  2022 vdir
-  -rwxr-xr-x 1 root root   71216 Mar 22 22:20 wdctl
-  lrwxrwxrwx 1 root root       8 Dec 19 01:33 ypdomainname -> hostname
-  -rwxr-xr-x 1 root root    1984 Apr  9  2022 zcat
-  -rwxr-xr-x 1 root root    1678 Apr  9  2022 zcmp
-  -rwxr-xr-x 1 root root    6460 Apr  9  2022 zdiff
-  -rwxr-xr-x 1 root root      29 Apr  9  2022 zegrep
-  -rwxr-xr-x 1 root root      29 Apr  9  2022 zfgrep
-  -rwxr-xr-x 1 root root    2081 Apr  9  2022 zforce
-  -rwxr-xr-x 1 root root    8103 Apr  9  2022 zgrep
-  -rwxr-xr-x 1 root root    2206 Apr  9  2022 zless
-  -rwxr-xr-x 1 root root    1842 Apr  9  2022 zmore
-  -rwxr-xr-x 1 root root    4577 Apr  9  2022 znew
-I: user script /srv/workspace/pbuilder/26567/tmp/hooks/D02_print_environment finished
+  -rwxr-xr-x 1 root root 1408088 Apr 24  2023 bash
+  -rwxr-xr-x 3 root root   38404 Sep 19  2022 bunzip2
+  -rwxr-xr-x 3 root root   38404 Sep 19  2022 bzcat
+  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzcmp -> bzdiff
+  -rwxr-xr-x 1 root root    2225 Sep 19  2022 bzdiff
+  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzegrep -> bzgrep
+  -rwxr-xr-x 1 root root    4893 Nov 28  2021 bzexe
+  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzfgrep -> bzgrep
+  -rwxr-xr-x 1 root root    3775 Sep 19  2022 bzgrep
+  -rwxr-xr-x 3 root root   38404 Sep 19  2022 bzip2
+  -rwxr-xr-x 1 root root   17892 Sep 19  2022 bzip2recover
+  lrwxrwxrwx 1 root root       6 Sep 19  2022 bzless -> bzmore
+  -rwxr-xr-x 1 root root    1297 Sep 19  2022 bzmore
+  -rwxr-xr-x 1 root root   42920 Sep 21  2022 cat
+  -rwxr-xr-x 1 root root   79816 Sep 21  2022 chgrp
+  -rwxr-xr-x 1 root root   67496 Sep 21  2022 chmod
+  -rwxr-xr-x 1 root root   79816 Sep 21  2022 chown
+  -rwxr-xr-x 1 root root  162024 Sep 21  2022 cp
+  -rwxr-xr-x 1 root root  136916 Jan  6  2023 dash
+  -rwxr-xr-x 1 root root  137160 Sep 21  2022 date
+  -rwxr-xr-x 1 root root  100364 Sep 21  2022 dd
+  -rwxr-xr-x 1 root root  108940 Sep 21  2022 df
+  -rwxr-xr-x 1 root root  162152 Sep 21  2022 dir
+  -rwxr-xr-x 1 root root   87760 Mar 24  2023 dmesg
+  lrwxrwxrwx 1 root root       8 Dec 20  2022 dnsdomainname -> hostname
+  lrwxrwxrwx 1 root root       8 Dec 20  2022 domainname -> hostname
+  -rwxr-xr-x 1 root root   38760 Sep 21  2022 echo
+  -rwxr-xr-x 1 root root      41 Jan 25  2023 egrep
+  -rwxr-xr-x 1 root root   34664 Sep 21  2022 false
+  -rwxr-xr-x 1 root root      41 Jan 25  2023 fgrep
+  -rwxr-xr-x 1 root root   84272 Mar 24  2023 findmnt
+  -rwsr-xr-x 1 root root   30240 Mar 23  2023 fusermount
+  -rwxr-xr-x 1 root root  218680 Jan 25  2023 grep
+  -rwxr-xr-x 2 root root    2346 Apr 10  2022 gunzip
+  -rwxr-xr-x 1 root root    6447 Apr 10  2022 gzexe
+  -rwxr-xr-x 1 root root  100952 Apr 10  2022 gzip
+  -rwxr-xr-x 1 root root   21916 Dec 20  2022 hostname
+  -rwxr-xr-x 1 root root   75756 Sep 21  2022 ln
+  -rwxr-xr-x 1 root root   55600 Mar 24  2023 login
+  -rwxr-xr-x 1 root root  162152 Sep 21  2022 ls
+  -rwxr-xr-x 1 root root  214568 Mar 24  2023 lsblk
+  -rwxr-xr-x 1 root root   96328 Sep 21  2022 mkdir
+  -rwxr-xr-x 1 root root   84008 Sep 21  2022 mknod
+  -rwxr-xr-x 1 root root   38792 Sep 21  2022 mktemp
+  -rwxr-xr-x 1 root root   63016 Mar 24  2023 more
+  -rwsr-xr-x 1 root root   58912 Mar 24  2023 mount
+  -rwxr-xr-x 1 root root   13856 Mar 24  2023 mountpoint
+  -rwxr-xr-x 1 root root  157932 Sep 21  2022 mv
+  lrwxrwxrwx 1 root root       8 Dec 20  2022 nisdomainname -> hostname
+  lrwxrwxrwx 1 root root      14 Apr  3  2023 pidof -> /sbin/killall5
+  -rwxr-xr-x 1 root root   38792 Sep 21  2022 pwd
+  lrwxrwxrwx 1 root root       4 Apr 24  2023 rbash -> bash
+  -rwxr-xr-x 1 root root   51080 Sep 21  2022 readlink
+  -rwxr-xr-x 1 root root   75720 Sep 21  2022 rm
+  -rwxr-xr-x 1 root root   51080 Sep 21  2022 rmdir
+  -rwxr-xr-x 1 root root   22308 Nov  3  2022 run-parts
+  -rwxr-xr-x 1 root root  133224 Jan  6  2023 sed
+  lrwxrwxrwx 1 root root       9 Jul 15 18:04 sh -> /bin/bash
+  -rwxr-xr-x 1 root root   38760 Sep 21  2022 sleep
+  -rwxr-xr-x 1 root root   87976 Sep 21  2022 stty
+  -rwsr-xr-x 1 root root   83492 Mar 24  2023 su
+  -rwxr-xr-x 1 root root   38792 Sep 21  2022 sync
+  -rwxr-xr-x 1 root root  598456 Apr  7  2023 tar
+  -rwxr-xr-x 1 root root   13860 Nov  3  2022 tempfile
+  -rwxr-xr-x 1 root root  120776 Sep 21  2022 touch
+  -rwxr-xr-x 1 root root   34664 Sep 21  2022 true
+  -rwxr-xr-x 1 root root   17892 Mar 23  2023 ulockmgr_server
+  -rwsr-xr-x 1 root root   30236 Mar 24  2023 umount
+  -rwxr-xr-x 1 root root   38760 Sep 21  2022 uname
+  -rwxr-xr-x 2 root root    2346 Apr 10  2022 uncompress
+  -rwxr-xr-x 1 root root  162152 Sep 21  2022 vdir
+  -rwxr-xr-x 1 root root   71216 Mar 24  2023 wdctl
+  lrwxrwxrwx 1 root root       8 Dec 20  2022 ypdomainname -> hostname
+  -rwxr-xr-x 1 root root    1984 Apr 10  2022 zcat
+  -rwxr-xr-x 1 root root    1678 Apr 10  2022 zcmp
+  -rwxr-xr-x 1 root root    6460 Apr 10  2022 zdiff
+  -rwxr-xr-x 1 root root      29 Apr 10  2022 zegrep
+  -rwxr-xr-x 1 root root      29 Apr 10  2022 zfgrep
+  -rwxr-xr-x 1 root root    2081 Apr 10  2022 zforce
+  -rwxr-xr-x 1 root root    8103 Apr 10  2022 zgrep
+  -rwxr-xr-x 1 root root    2206 Apr 10  2022 zless
+  -rwxr-xr-x 1 root root    1842 Apr 10  2022 zmore
+  -rwxr-xr-x 1 root root    4577 Apr 10  2022 znew
+I: user script /srv/workspace/pbuilder/93232/tmp/hooks/D02_print_environment finished
  -> Attempting to satisfy build-dependencies
  -> Creating pbuilder-satisfydepends-dummy package
 Package: pbuilder-satisfydepends-dummy
@@ -393,7 +2925,7 @@
 Get: 188 http://deb.debian.org/debian bookworm/main i386 qtbase5-dev-tools i386 5.15.8+dfsg-11 [846 kB]
 Get: 189 http://deb.debian.org/debian bookworm/main i386 qtbase5-dev i386 5.15.8+dfsg-11 [1122 kB]
 Get: 190 http://deb.debian.org/debian bookworm/main i386 qttools5-dev-tools i386 5.15.8-2 [1144 kB]
-Fetched 162 MB in 4s (38.1 MB/s)
+Fetched 162 MB in 2s (68.1 MB/s)
 debconf: delaying package configuration, since apt-utils is not installed
 Selecting previously unselected package libglib2.0-0:i386.
 (Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 19599 files and directories currently installed.)
@@ -1174,8 +3706,19 @@
 Writing extended state information...
 Building tag database...
  -> Finished parsing the build-deps
+Reading package lists...
+Building dependency tree...
+Reading state information...
+usrmerge is already the newest version (35).
+0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
 I: Building the package
-I: Running cd /build/clustalx-2.1+lgpl/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S  > ../clustalx_2.1+lgpl-9_source.changes
+I: user script /srv/workspace/pbuilder/93232/tmp/hooks/A99_set_merged_usr starting
+Re-configuring usrmerge...
+removed '/etc/unsupported-skip-usrmerge-conversion'
+The system has been successfully converted.
+I: user script /srv/workspace/pbuilder/93232/tmp/hooks/A99_set_merged_usr finished
+hostname: Name or service not known
+I: Running cd /build/clustalx-2.1+lgpl/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S  > ../clustalx_2.1+lgpl-9_source.changes
 dpkg-buildpackage: info: source package clustalx
 dpkg-buildpackage: info: source version 2.1+lgpl-9
 dpkg-buildpackage: info: source distribution unstable
@@ -1205,7 +3748,7 @@
        -e "s:LFLAGS *= .*:& -Wl,-z,relro -Wl,-z,now:" Makefile
 make[1]: Leaving directory '/build/clustalx-2.1+lgpl'
    dh_auto_build
-	make -j8
+	make -j15
 make[1]: Entering directory '/build/clustalx-2.1+lgpl'
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentFormatOptions.o AlignmentFormatOptions.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentParameters.o AlignmentParameters.cpp
@@ -1215,6 +3758,13 @@
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o BootstrapTreeDialog.o BootstrapTreeDialog.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ColorFileXmlParser.o ColorFileXmlParser.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ColorParameters.o ColorParameters.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp
 ColorFileXmlParser.cpp:74:13: warning: multi-line comment [-Wcomment]
    74 |             //                     tr("colorrules not found in the parameter file, using\
       |             ^
@@ -1222,6 +3772,17 @@
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
                  from HardCodedColorScheme.h:8,
+                 from HardCodedColorScheme.cpp:1:
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/alignment/Alignment.h:42,
+                 from ClustalQtParams.h:13,
+                 from HardCodedColorScheme.h:8,
                  from ColorParameters.h:11,
                  from ColorParameters.cpp:1:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
@@ -1268,33 +3829,25 @@
 ColorParameters.cpp:251:37: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<residueColors>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   251 |     if(colorNum > 0 && colorNum - 1 < colorPar.size())
       |                        ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ColumnScoreParams.o ColumnScoreParams.cpp
-In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
-                 from AlignmentParameters.cpp:22:
-clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-AlignmentParameters.cpp: In member function 'virtual void AlignmentParameters::showEvent(QShowEvent*)':
-AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter]
-   48 | void AlignmentParameters::showEvent(QShowEvent* event)
-      |                                     ~~~~~~~~~~~~^~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
-                 from AlignmentWidget.h:41,
-                 from AlignmentWidget.cpp:49:
+                 from ClustalQtParams.h:13,
+                 from HelpDisplayWidget.h:18,
+                 from HelpDisplayWidget.cpp:15:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
-                 from AlignmentViewerWidget.h:36,
-                 from AlignmentViewerWidget.cpp:66:
+                 from AlignmentWidget.h:41,
+                 from AlignmentWidget.cpp:49:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
@@ -1348,6 +3901,14 @@
 AlignmentWidget.cpp:569:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<QPixmap, std::allocator<QPixmap> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   569 |                     if(selectedRes >= selectedColoredRes->size())
       |                        ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
+                 from ColumnScoreParams.cpp:23:
+clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
 AlignmentWidget.cpp: In member function 'void AlignmentWidget::calcConserveInfo()':
 AlignmentWidget.cpp:689:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   689 |             for(int j = 1; j <= strongGroup.size(); j++)
@@ -1367,6 +3928,10 @@
 AlignmentWidget.cpp:737:42: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   737 |                         for(int k = 1; k <= weakGroup.size(); k++)
       |                                        ~~^~~~~~~~~~~~~~~~~~~
+ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)':
+ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter]
+   51 | void ColumnScoreParams::showEvent(QShowEvent* event)
+      |                                   ~~~~~~~~~~~~^~~~~
 AlignmentWidget.cpp:760:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   760 |                 for(int k = 1; k <= strongGroup.size(); k++)
       |                                ~~^~~~~~~~~~~~~~~~~~~~~
@@ -1415,6 +3980,86 @@
 /usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here
   110 |     int width(QChar) const;
       |         ^~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp
+In file included from main.cpp:21:
+clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/alignment/Alignment.h:42,
+                 from ClustalQtParams.h:13,
+                 from BootstrapTreeDialog.h:11,
+                 from BootstrapTreeDialog.cpp:18:
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+BootstrapTreeDialog.h:70:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   70 |     auto_ptr<clustalw::TreeNames> treeFileNames;
+      |     ^~~~~~~~
+In file included from /usr/include/c++/12/memory:76,
+                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71,
+                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48,
+                 from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48,
+                 from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1,
+                 from BootstrapTreeDialog.cpp:8:
+/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
+   64 |   template<typename> class auto_ptr;
+      |                            ^~~~~~~~
+In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/alignment/Alignment.h:42,
+                 from ClustalQtParams.h:13,
+                 from PostscriptFileParams.h:4,
+                 from PostscriptFileParams.cpp:1:
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/alignment/Alignment.h:42,
+                 from AlignmentViewerWidget.h:36,
+                 from AlignmentViewerWidget.cpp:66:
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)':
+HistogramWidget.cpp:180:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
+  180 |             if(column >= 0 && column < arrayOfHeights->size())
+      |                               ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
+HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
+  198 |             if(column >= 0 && column < arrayOfHeights->size())
+      |                               ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
+HistogramWidget.cpp:208:47: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
+  208 |                             (fontMetrics.width(QString::number(rulerNum))) / 2;
+      |                              ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/i386-linux-gnu/qt5/QtWidgets/qwidget.h:50,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qframe.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qlabel.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QLabel:1,
+                 from HistogramWidget.h:29,
+                 from HistogramWidget.cpp:23:
+/usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here
+  106 |     int width(const QString &, int len = -1) const;
+      |         ^~~~~
+HistogramWidget.cpp:241:61: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
+  241 |                                           (fontMetrics.width(QString::number(0))) / 2, yPos, boxWidth,
+      |                                            ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
+/usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here
+  106 |     int width(const QString &, int len = -1) const;
+      |         ^~~~~
 In file included from AlignmentViewerWidget.cpp:68:
 clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
    68 |         bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
@@ -1496,134 +4141,18 @@
 AlignmentViewerWidget.cpp:781:58: warning: unused parameter 'event' [-Wunused-parameter]
   781 | void AlignmentViewerWidget::resizeEvent ( QResizeEvent * event )
       |                                           ~~~~~~~~~~~~~~~^~~~~
-In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/alignment/Alignment.h:42,
-                 from ClustalQtParams.h:13,
-                 from BootstrapTreeDialog.h:11,
-                 from BootstrapTreeDialog.cpp:18:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-BootstrapTreeDialog.h:70:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   70 |     auto_ptr<clustalw::TreeNames> treeFileNames;
-      |     ^~~~~~~~
-In file included from /usr/include/c++/12/memory:76,
-                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71,
-                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48,
-                 from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48,
-                 from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1,
-                 from BootstrapTreeDialog.cpp:8:
-/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
-   64 |   template<typename> class auto_ptr;
-      |                            ^~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileDialog.o FileDialog.cpp
-In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/alignment/Alignment.h:42,
-                 from ClustalQtParams.h:13,
-                 from HardCodedColorScheme.h:8,
-                 from ColorParameters.h:11,
-                 from ColorFileXmlParser.h:9,
-                 from ColorFileXmlParser.cpp:3:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)':
-ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter]
-   85 |                             QTreeWidgetItem *parentItem)
-      |                             ~~~~~~~~~~~~~~~~~^~~~~~~~~~
-ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)':
-ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter]
-  138 | void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem)
-      |                                                                     ~~~~~~~~~~~~~~~~~^~~~~~~~~~
-ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)':
-ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter]
-  175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem)
-      |                                                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~
-In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/alignment/Alignment.h:42,
-                 from ClustalQtParams.h:13,
-                 from AlignOutputFileNames.h:10,
-                 from AlignOutputFileNames.cpp:26:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-AlignOutputFileNames.h:106:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  106 |     auto_ptr<clustalw::AlignmentFileNames> outFileNames;
-      |     ^~~~~~~~
-In file included from /usr/include/c++/12/memory:76,
-                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71,
-                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48,
-                 from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48,
-                 from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1,
-                 from AlignOutputFileNames.cpp:16:
-/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
-   64 |   template<typename> class auto_ptr;
-      |                            ^~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HardCodedColorScheme.o HardCodedColorScheme.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HelpDisplayWidget.o HelpDisplayWidget.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o HistogramWidget.o HistogramWidget.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o KeyController.o KeyController.cpp
-In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/alignment/Alignment.h:42,
-                 from ClustalQtParams.h:13,
-                 from HardCodedColorScheme.h:8,
-                 from HardCodedColorScheme.cpp:1:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoringSegParams.o LowScoringSegParams.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o main.o main.cpp
 In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
-                 from ColumnScoreParams.cpp:23:
-clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-ColumnScoreParams.cpp: In member function 'virtual void ColumnScoreParams::showEvent(QShowEvent*)':
-ColumnScoreParams.cpp:51:47: warning: unused parameter 'event' [-Wunused-parameter]
-   51 | void ColumnScoreParams::showEvent(QShowEvent* event)
-      |                                   ~~~~~~~~~~~~^~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o mainwindow.o mainwindow.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PairwiseParams.o PairwiseParams.cpp
-In file included from main.cpp:21:
+                 from AlignmentParameters.cpp:22:
 clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/alignment/Alignment.h:42,
-                 from ClustalQtParams.h:13,
-                 from HelpDisplayWidget.h:18,
-                 from HelpDisplayWidget.cpp:15:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PostscriptFileParams.o PostscriptFileParams.cpp
+AlignmentParameters.cpp: In member function 'virtual void AlignmentParameters::showEvent(QShowEvent*)':
+AlignmentParameters.cpp:48:49: warning: unused parameter 'event' [-Wunused-parameter]
+   48 | void AlignmentParameters::showEvent(QShowEvent* event)
+      |                                     ~~~~~~~~~~~~^~~~~
 In file included from clustalW/Clustal.h:18,
                  from mainwindow.h:45,
                  from main.cpp:24:
@@ -1698,45 +4227,70 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProteinGapParameters.o ProteinGapParameters.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PSPrinter.o PSPrinter.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
-                 from PostscriptFileParams.h:4,
-                 from PostscriptFileParams.cpp:1:
+                 from HardCodedColorScheme.h:8,
+                 from ColorParameters.h:11,
+                 from ColorFileXmlParser.h:9,
+                 from ColorFileXmlParser.cpp:3:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp
-HistogramWidget.cpp: In member function 'void HistogramWidget::drawContents(QPainter*, int, int, int, int)':
-HistogramWidget.cpp:180:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
-  180 |             if(column >= 0 && column < arrayOfHeights->size())
-      |                               ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
-HistogramWidget.cpp:198:38: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
-  198 |             if(column >= 0 && column < arrayOfHeights->size())
-      |                               ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
-HistogramWidget.cpp:208:47: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
-  208 |                             (fontMetrics.width(QString::number(rulerNum))) / 2;
-      |                              ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/i386-linux-gnu/qt5/QtWidgets/qwidget.h:50,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qframe.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qlabel.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QLabel:1,
-                 from HistogramWidget.h:29,
-                 from HistogramWidget.cpp:23:
-/usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here
-  106 |     int width(const QString &, int len = -1) const;
-      |         ^~~~~
-HistogramWidget.cpp:241:61: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
-  241 |                                           (fontMetrics.width(QString::number(0))) / 2, yPos, boxWidth,
-      |                                            ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
-/usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here
-  106 |     int width(const QString &, int len = -1) const;
-      |         ^~~~~
+In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/alignment/Alignment.h:42,
+                 from ClustalQtParams.h:13,
+                 from AlignOutputFileNames.h:10,
+                 from AlignOutputFileNames.cpp:26:
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseRGBIndex(const QDomElement&, QTreeWidgetItem*)':
+ColorFileXmlParser.cpp:85:46: warning: unused parameter 'parentItem' [-Wunused-parameter]
+   85 |                             QTreeWidgetItem *parentItem)
+      |                             ~~~~~~~~~~~~~~~~~^~~~~~~~~~
+ColorFileXmlParser.cpp: In member function 'void ColorFileXmlParser::parseConsensus(const QDomElement&, QTreeWidgetItem*)':
+ColorFileXmlParser.cpp:138:86: warning: unused parameter 'parentItem' [-Wunused-parameter]
+  138 | void ColorFileXmlParser::parseConsensus(const QDomElement &element, QTreeWidgetItem *parentItem)
+      |                                                                     ~~~~~~~~~~~~~~~~~^~~~~~~~~~
+ColorFileXmlParser.cpp: In member function 'int ColorFileXmlParser::parseColorRule(const QDomElement&, QTreeWidgetItem*)':
+ColorFileXmlParser.cpp:175:85: warning: unused parameter 'parentItem' [-Wunused-parameter]
+  175 | int ColorFileXmlParser::parseColorRule(const QDomElement &element, QTreeWidgetItem *parentItem)
+      |                                                                    ~~~~~~~~~~~~~~~~~^~~~~~~~~~
+AlignOutputFileNames.h:106:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  106 |     auto_ptr<clustalw::AlignmentFileNames> outFileNames;
+      |     ^~~~~~~~
+In file included from /usr/include/c++/12/memory:76,
+                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71,
+                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48,
+                 from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48,
+                 from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1,
+                 from AlignOutputFileNames.cpp:16:
+/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
+   64 |   template<typename> class auto_ptr;
+      |                            ^~~~~~~~
+In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
+                 from LowScoringSegParams.cpp:22:
+clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)':
+LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter]
+   51 | void LowScoringSegParams::showEvent(QShowEvent* event)
+      |                                     ~~~~~~~~~~~~^~~~~
 HelpDisplayWidget.cpp: In member function 'std::string* HelpDisplayWidget::loadHelpInformation(char)':
 HelpDisplayWidget.cpp:147:29: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
   147 |     catch(ifstream::failure e)
@@ -1829,6 +4383,7 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o QTUtility.o QTUtility.cpp
 In file included from mainwindow.cpp:99:
 WritePostscriptFile.h:88:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
    88 |     auto_ptr<PostscriptFileParams> params;
@@ -1861,23 +4416,13 @@
 mainwindow.cpp:198:40: warning: unused parameter 'event' [-Wunused-parameter]
   198 | void MainWindow::showEvent(QShowEvent* event)
       |                            ~~~~~~~~~~~~^~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp
 mainwindow.cpp: In member function 'void MainWindow::writeViewer1AsPostscript(int)':
 mainwindow.cpp:1454:47: warning: unused parameter 'type' [-Wunused-parameter]
  1454 | void MainWindow::writeViewer1AsPostscript(int type)
       |                                           ~~~~^~~~
-In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
-                 from LowScoringSegParams.cpp:22:
-clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-LowScoringSegParams.cpp: In member function 'virtual void LowScoringSegParams::showEvent(QShowEvent*)':
-LowScoringSegParams.cpp:51:49: warning: unused parameter 'event' [-Wunused-parameter]
-   51 | void LowScoringSegParams::showEvent(QShowEvent* event)
-      |                                     ~~~~~~~~~~~~^~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Resources.o Resources.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp
 In file included from clustalW/substitutionMatrix/globalmatrix.h:8,
                  from PairwiseParams.cpp:23:
 clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
@@ -1890,61 +4435,40 @@
 PairwiseParams.cpp:74:44: warning: unused parameter 'event' [-Wunused-parameter]
    74 | void PairwiseParams::showEvent(QShowEvent* event)
       |                                ~~~~~~~~~~~~^~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SaveSeqFile.o SaveSeqFile.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SearchForString.o SearchForString.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
-                 from ClustalQtParams.h:13,
-                 from HardCodedColorScheme.h:8,
-                 from ColorParameters.h:11,
-                 from PSPrinter.h:11,
-                 from PSPrinter.cpp:20:
+                 from clustalW/alignment/Alignment.cpp:25:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)':
-PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
-  207 |                 if(res.isLetter() && resNumber.size() > i - data->firstSeq)
-      |                                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
-PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
-  307 |                             if(res.isLetter() && resNumber.size() > seq)
-      |                                                  ~~~~~~~~~~~~~~~~~^~~~~
-PSPrinter.cpp:421:67: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
-  421 |                             if(res.isLetter() && resNumber.size() > i)
-      |                                                  ~~~~~~~~~~~~~~~~~^~~
-PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable]
-   55 |     int err;
-      |         ^~~
-PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable]
-   73 |     int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local
-      |         ^~~~~~~
-PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable]
-   74 |     int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local
-      |         ^~~~~~~
-PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)':
-PSPrinter.cpp:587:32: warning: comparison of integer expressions of different signedness: 'std::vector<QString>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
-  587 |     if(data->nameHeader.size() > ix)
-      |        ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
-PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)':
-PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
-  730 |     for(i = fr; i <= lr && i < ruler.length(); i++)
-      |                            ~~^~~~~~~~~~~~~~~~
-PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)':
-PSPrinter.cpp:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
-  789 |     for(i = fr + 1; i <= lr && i < data->histogram->size(); i++)
-      |                                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
-PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable]
-  781 |     int psX, psY, curveBottom;
-      |              ^~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SecStructOptions.o SecStructOptions.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SeqNameWidget.o SeqNameWidget.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeFormatOptions.o TreeFormatOptions.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeOutputFileNames.o TreeOutputFileNames.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o WritePostscriptFile.o WritePostscriptFile.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Clustal.o clustalW/Clustal.cpp
+clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()':
+clustalW/alignment/Alignment.cpp:47:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+   47 |     register int sl;                /* which have  code = gap_pos2  */
+      |                  ^~
+clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()':
+clustalW/alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+  122 |     register int sl;                /* which have  code = gap_pos2  */
+      |                  ^~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp
+clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()':
+clustalW/alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+  617 |     register int sl;
+      |                  ^~
+clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
+clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
+ 1715 |     SeqArray::iterator posToAddTo = sectionToRealign.begin();
+      |                        ^~~~~~~~~~
 In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/fileInput/../alignment/Alignment.h:42,
                  from clustalW/fileInput/FileReader.h:12,
@@ -2076,30 +4600,24 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
-                 from ClustalQtParams.h:13,
-                 from SaveSeqFile.h:9,
-                 from SaveSeqFile.cpp:23:
+                 from clustalW/alignment/AlignmentOutput.h:24,
+                 from clustalW/alignment/AlignmentOutput.cpp:27:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-In file included from SaveSeqFile.cpp:26:
 clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
    68 |         bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
       |                               ^~~~~~~~
 In file included from /usr/include/c++/12/memory:76,
-                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71,
-                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48,
-                 from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48,
-                 from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1,
-                 from SaveSeqFile.cpp:14:
+                 from clustalW/alignment/AlignmentOutput.h:20:
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
@@ -2151,60 +4669,113 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
+clustalW/alignment/AlignmentOutput.cpp:512:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  512 | bool AlignmentOutput::openExplicitFile(auto_ptr<ofstream>& outFile, string fileName)
+      |                                        ^~~~~~~~
+/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
+   64 |   template<typename> class auto_ptr;
+      |                            ^~~~~~~~
+clustalW/alignment/AlignmentOutput.cpp:535:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  535 | string AlignmentOutput::openOutputFile(auto_ptr<ofstream>& outFile, string prompt,
+      |                                        ^~~~~~~~
+/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
+   64 |   template<typename> class auto_ptr;
+      |                            ^~~~~~~~
+clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion)':
+clustalW/alignment/AlignmentOutput.cpp:673:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
+  673 |     catch(VectorOutOfRange e)
+      |                            ^
+clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)':
+clustalW/alignment/AlignmentOutput.cpp:868:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
+  868 |     catch(VectorOutOfRange e)
+      |                            ^
+clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::phylipOut(clustalw::Alignment*, clustalw::outputRegion)':
+clustalW/alignment/AlignmentOutput.cpp:1027:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
+ 1027 |     catch(VectorOutOfRange e)
+      |                            ^
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/alignment/Alignment.h:42,
-                 from SeqNameWidget.h:41,
-                 from SeqNameWidget.cpp:59:
+                 from clustalW/alignment/ObjectiveScore.h:15,
+                 from clustalW/alignment/ObjectiveScore.cpp:10:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)':
-SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable]
-  375 |     QRect redrawRect = event->rect();
-      |           ^~~~~~~~~~
-SeqNameWidget.cpp: In member function 'int SeqNameWidget::setMaxNameLength()':
-SeqNameWidget.cpp:443:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
-  443 |             int length = fontMetrics.width(QString(name.c_str()));
-      |                          ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
-In file included from /usr/include/i386-linux-gnu/qt5/QtGui/QtGui:26,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3,
-                 from SeqNameWidget.cpp:58:
-/usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here
-  106 |     int width(const QString &, int len = -1) const;
-      |         ^~~~~
+clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)':
+clustalW/alignment/AlignmentOutput.cpp:1156:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
+ 1156 |     catch(VectorOutOfRange e)
+      |                            ^
+clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)':
+clustalW/alignment/AlignmentOutput.cpp:1445:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
+ 1445 |     catch(VectorOutOfRange e)
+      |                            ^
+clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)':
+clustalW/alignment/AlignmentOutput.cpp:1560:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
+ 1560 |     catch(VectorOutOfRange e)
+      |                            ^
+clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion)':
+clustalW/alignment/AlignmentOutput.cpp:2095:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
+ 2095 |     catch(VectorOutOfRange e)
+      |                            ^
+clustalW/alignment/AlignmentOutput.cpp:2102:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
+ 2102 |     catch(exception e)
+      |                     ^
+clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)':
+clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
+ 2351 |     catch(VectorOutOfRange e)
+      |                            ^
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
-                 from TreeOutputFileNames.h:10,
-                 from TreeOutputFileNames.cpp:17:
+                 from HardCodedColorScheme.h:8,
+                 from ColorParameters.h:11,
+                 from PSPrinter.h:11,
+                 from PSPrinter.cpp:20:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-TreeOutputFileNames.h:73:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   73 |     auto_ptr<clustalw::TreeNames> treeFileNames;
-      |     ^~~~~~~~
-In file included from /usr/include/c++/12/memory:76,
-                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71,
-                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48,
-                 from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48,
-                 from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44,
-                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1,
-                 from TreeOutputFileNames.cpp:7:
-/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
-   64 |   template<typename> class auto_ptr;
-      |                            ^~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Help.o clustalW/Help.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Alignment.o clustalW/alignment/Alignment.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentOutput.o clustalW/alignment/AlignmentOutput.cpp
+PSPrinter.cpp: In member function 'void PSPrinter::writePSFile(PostscriptFileParams*)':
+PSPrinter.cpp:207:55: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
+  207 |                 if(res.isLetter() && resNumber.size() > i - data->firstSeq)
+      |                                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
+PSPrinter.cpp:307:67: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
+  307 |                             if(res.isLetter() && resNumber.size() > seq)
+      |                                                  ~~~~~~~~~~~~~~~~~^~~~~
+PSPrinter.cpp:421:67: warning: comparison of integer expressions of different signedness: 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
+  421 |                             if(res.isLetter() && resNumber.size() > i)
+      |                                                  ~~~~~~~~~~~~~~~~~^~~
+PSPrinter.cpp:55:9: warning: unused variable 'err' [-Wunused-variable]
+   55 |     int err;
+      |         ^~~
+PSPrinter.cpp:73:9: warning: unused variable 'gapPos1' [-Wunused-variable]
+   73 |     int gapPos1 = clustalw::userParameters->getGapPos1(); // Mark: 22-1-2007 new local
+      |         ^~~~~~~
+PSPrinter.cpp:74:9: warning: unused variable 'gapPos2' [-Wunused-variable]
+   74 |     int gapPos2 = clustalw::userParameters->getGapPos2(); // Mark: 22-1-2007 new local
+      |         ^~~~~~~
+PSPrinter.cpp: In member function 'void PSPrinter::printHeaderLine(std::ofstream*, int, int, int)':
+PSPrinter.cpp:587:32: warning: comparison of integer expressions of different signedness: 'std::vector<QString>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
+  587 |     if(data->nameHeader.size() > ix)
+      |        ~~~~~~~~~~~~~~~~~~~~~~~~^~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp
+PSPrinter.cpp: In member function 'void PSPrinter::printFooterLine(std::ofstream*, int, int)':
+PSPrinter.cpp:730:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
+  730 |     for(i = fr; i <= lr && i < ruler.length(); i++)
+      |                            ~~^~~~~~~~~~~~~~~~
+PSPrinter.cpp: In member function 'void PSPrinter::printQualityCurve(std::ofstream*, int, int, int)':
+PSPrinter.cpp:789:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
+  789 |     for(i = fr + 1; i <= lr && i < data->histogram->size(); i++)
+      |                                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
+PSPrinter.cpp:781:14: warning: unused variable 'psY' [-Wunused-variable]
+  781 |     int psX, psY, curveBottom;
+      |              ^~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
@@ -2286,49 +4857,63 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
-                 from clustalW/alignment/Alignment.cpp:25:
+                 from SeqNameWidget.h:41,
+                 from SeqNameWidget.cpp:59:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile1()':
-clustalW/alignment/Alignment.cpp:47:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-   47 |     register int sl;                /* which have  code = gap_pos2  */
-      |                  ^~
-clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetProfile2()':
-clustalW/alignment/Alignment.cpp:122:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-  122 |     register int sl;                /* which have  code = gap_pos2  */
-      |                  ^~
-clustalW/alignment/Alignment.cpp: In member function 'void clustalw::Alignment::resetAlign()':
-clustalW/alignment/Alignment.cpp:617:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-  617 |     register int sl;
-      |                  ^~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ObjectiveScore.o clustalW/alignment/ObjectiveScore.cpp
-clustalW/alignment/Alignment.cpp: In member function 'bool clustalw::Alignment::keepPortionOfSeqArray(int, int)':
-clustalW/alignment/Alignment.cpp:1715:24: warning: variable 'posToAddTo' set but not used [-Wunused-but-set-variable]
- 1715 |     SeqArray::iterator posToAddTo = sectionToRealign.begin();
-      |                        ^~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Sequence.o clustalW/alignment/Sequence.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalFileParser.o clustalW/fileInput/ClustalFileParser.cpp
+SeqNameWidget.cpp: In member function 'virtual void SeqNameWidget::paintEvent(QPaintEvent*)':
+SeqNameWidget.cpp:375:11: warning: variable 'redrawRect' set but not used [-Wunused-but-set-variable]
+  375 |     QRect redrawRect = event->rect();
+      |           ^~~~~~~~~~
+SeqNameWidget.cpp: In member function 'int SeqNameWidget::setMaxNameLength()':
+SeqNameWidget.cpp:443:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations]
+  443 |             int length = fontMetrics.width(QString(name.c_str()));
+      |                          ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
+In file included from /usr/include/i386-linux-gnu/qt5/QtGui/QtGui:26,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgetsDepends:4,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QtWidgets:3,
+                 from SeqNameWidget.cpp:58:
+/usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here
+  106 |     int width(const QString &, int len = -1) const;
+      |         ^~~~~
+clustalW/fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()':
+clustalW/fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+   37 |     register int i;
+      |                  ^
+clustalW/fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+   38 |     register char c;
+      |                   ^
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
-                 from clustalW/alignment/AlignmentOutput.h:24,
-                 from clustalW/alignment/AlignmentOutput.cpp:27:
+                 from ClustalQtParams.h:13,
+                 from SaveSeqFile.h:9,
+                 from SaveSeqFile.cpp:23:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
+In file included from SaveSeqFile.cpp:26:
 clustalW/alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
    68 |         bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
       |                               ^~~~~~~~
 In file included from /usr/include/c++/12/memory:76,
-                 from clustalW/alignment/AlignmentOutput.h:20:
+                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71,
+                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48,
+                 from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48,
+                 from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1,
+                 from SaveSeqFile.cpp:14:
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
@@ -2380,76 +4965,33 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/alignment/AlignmentOutput.cpp:512:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  512 | bool AlignmentOutput::openExplicitFile(auto_ptr<ofstream>& outFile, string fileName)
-      |                                        ^~~~~~~~
-/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
-   64 |   template<typename> class auto_ptr;
-      |                            ^~~~~~~~
-clustalW/alignment/AlignmentOutput.cpp:535:40: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  535 | string AlignmentOutput::openOutputFile(auto_ptr<ofstream>& outFile, string prompt,
-      |                                        ^~~~~~~~
-/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
-   64 |   template<typename> class auto_ptr;
-      |                            ^~~~~~~~
-clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::fastaOut(clustalw::Alignment*, clustalw::outputRegion)':
-clustalW/alignment/AlignmentOutput.cpp:673:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
-  673 |     catch(VectorOutOfRange e)
-      |                            ^
-clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gcgOut(clustalw::Alignment*, clustalw::outputRegion)':
-clustalW/alignment/AlignmentOutput.cpp:868:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
-  868 |     catch(VectorOutOfRange e)
-      |                            ^
-clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::phylipOut(clustalw::Alignment*, clustalw::outputRegion)':
-clustalW/alignment/AlignmentOutput.cpp:1027:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
- 1027 |     catch(VectorOutOfRange e)
-      |                            ^
-clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nexusOut(clustalw::Alignment*, clustalw::outputRegion)':
-clustalW/alignment/AlignmentOutput.cpp:1156:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
- 1156 |     catch(VectorOutOfRange e)
-      |                            ^
-clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::gdeOut(clustalw::Alignment*, clustalw::outputRegion)':
-clustalW/alignment/AlignmentOutput.cpp:1445:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
- 1445 |     catch(VectorOutOfRange e)
-      |                            ^
-clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::nbrfOut(clustalw::Alignment*, clustalw::outputRegion)':
-clustalW/alignment/AlignmentOutput.cpp:1560:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
- 1560 |     catch(VectorOutOfRange e)
-      |                            ^
-clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::clustalOut(clustalw::Alignment*, clustalw::outputRegion)':
-clustalW/alignment/AlignmentOutput.cpp:2095:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
- 2095 |     catch(VectorOutOfRange e)
-      |                            ^
-clustalW/alignment/AlignmentOutput.cpp:2102:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
- 2102 |     catch(exception e)
-      |                     ^
-clustalW/alignment/AlignmentOutput.cpp: In member function 'void clustalw::AlignmentOutput::findRangeValues(clustalw::Alignment*, clustalw::rangeNum*, int, int, int)':
-clustalW/alignment/AlignmentOutput.cpp:2351:28: warning: catching polymorphic type 'class clustalw::VectorOutOfRange' by value [-Wcatch-value=]
- 2351 |     catch(VectorOutOfRange e)
-      |                            ^
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o EMBLFileParser.o clustalW/fileInput/EMBLFileParser.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/alignment/ObjectiveScore.h:15,
-                 from clustalW/alignment/ObjectiveScore.cpp:10:
+                 from clustalW/alignment/Alignment.h:42,
+                 from ClustalQtParams.h:13,
+                 from TreeOutputFileNames.h:10,
+                 from TreeOutputFileNames.cpp:17:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileParser.o clustalW/fileInput/FileParser.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FileReader.o clustalW/fileInput/FileReader.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o GDEFileParser.o clustalW/fileInput/GDEFileParser.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o InFileStream.o clustalW/fileInput/InFileStream.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o MSFFileParser.o clustalW/fileInput/MSFFileParser.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp
-clustalW/fileInput/FileParser.cpp: In member function 'void clustalw::FileParser::fillCharTab()':
-clustalW/fileInput/FileParser.cpp:37:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-   37 |     register int i;
-      |                  ^
-clustalW/fileInput/FileParser.cpp:38:19: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-   38 |     register char c;
-      |                   ^
+TreeOutputFileNames.h:73:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   73 |     auto_ptr<clustalw::TreeNames> treeFileNames;
+      |     ^~~~~~~~
+In file included from /usr/include/c++/12/memory:76,
+                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer_impl.h:71,
+                 from /usr/include/i386-linux-gnu/qt5/QtCore/qsharedpointer.h:48,
+                 from /usr/include/i386-linux-gnu/qt5/QtGui/qpixmap.h:48,
+                 from /usr/include/i386-linux-gnu/qt5/QtGui/qicon.h:46,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractbutton.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/qpushbutton.h:44,
+                 from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPushButton:1,
+                 from TreeOutputFileNames.cpp:7:
+/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
+   64 |   template<typename> class auto_ptr;
+      |                            ^~~~~~~~
 In file included from clustalW/fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/fileInput/../alignment/Alignment.h:42,
                  from clustalW/fileInput/FileReader.h:12,
@@ -2486,25 +5028,6 @@
 clustalW/fileInput/FileReader.cpp:555:21: warning: catching polymorphic type 'class std::exception' by value [-Wcatch-value=]
   555 |     catch(exception ex)
       |                     ^~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp
-clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual clustalw::Sequence clustalw::PearsonFileParser::getSeq(int, std::string*)':
-clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter]
-  199 |     Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq)
-      |                                                    ~~~~~~~~^~~~~~~~~~~~
-clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual void clustalw::PearsonFileParser::getSecStructure(std::vector<char>&, std::vector<char>&, std::string&, int&, int)':
-clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
-  444 | void PearsonFileParser::getSecStructure(vector<char>& gapPenaltyMask,
-      |                                         ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
-clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter]
-  445 |                          vector<char>& secStructMask, string& secStructName,
-      |                          ~~~~~~~~~~~~~~^~~~~~~~~~~~~
-clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter]
-  445 |                          vector<char>& secStructMask, string& secStructName,
-      |                                                       ~~~~~~~~^~~~~~~~~~~~~
-clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter]
-  446 |                           int &structPenalties, int length)
-      |                                                 ~~~~^~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp
 clustalW/fileInput/MSFFileParser.cpp: In member function 'virtual std::vector<clustalw::Sequence> clustalw::MSFFileParser::getSeqRange(int, int, std::string*)':
 clustalW/fileInput/MSFFileParser.cpp:34:79: warning: unused parameter 'offendingSeq' [-Wunused-parameter]
    34 |     vector<Sequence> MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq)
@@ -2522,11 +5045,31 @@
 clustalW/fileInput/MSFFileParser.cpp:247:86: warning: unused parameter 'length' [-Wunused-parameter]
   247 |                                     string& secStructName, int &structPenalties, int length)
       |                                                                                  ~~~~^~~~~~
-clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector<char>&, std::vector<char>&, std::string&, int&, int)':
-clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
-  240 | void RSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
-      |                                     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PearsonFileParser.o clustalW/fileInput/PearsonFileParser.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o PIRFileParser.o clustalW/fileInput/PIRFileParser.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RSFFileParser.o clustalW/fileInput/RSFFileParser.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClustalWResources.o clustalW/general/ClustalWResources.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp
+clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual clustalw::Sequence clustalw::PearsonFileParser::getSeq(int, std::string*)':
+clustalW/fileInput/PearsonFileParser.cpp:199:60: warning: unused parameter 'offendingSeq' [-Wunused-parameter]
+  199 |     Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq)
+      |                                                    ~~~~~~~~^~~~~~~~~~~~
+clustalW/fileInput/PearsonFileParser.cpp: In member function 'virtual void clustalw::PearsonFileParser::getSecStructure(std::vector<char>&, std::vector<char>&, std::string&, int&, int)':
+clustalW/fileInput/PearsonFileParser.cpp:444:55: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
+  444 | void PearsonFileParser::getSecStructure(vector<char>& gapPenaltyMask,
+      |                                         ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
+clustalW/fileInput/PearsonFileParser.cpp:445:40: warning: unused parameter 'secStructMask' [-Wunused-parameter]
+  445 |                          vector<char>& secStructMask, string& secStructName,
+      |                          ~~~~~~~~~~~~~~^~~~~~~~~~~~~
+clustalW/fileInput/PearsonFileParser.cpp:445:63: warning: unused parameter 'secStructName' [-Wunused-parameter]
+  445 |                          vector<char>& secStructMask, string& secStructName,
+      |                                                       ~~~~~~~~^~~~~~~~~~~~~
+clustalW/fileInput/PearsonFileParser.cpp:446:53: warning: unused parameter 'length' [-Wunused-parameter]
+  446 |                           int &structPenalties, int length)
+      |                                                 ~~~~^~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp
 clustalW/fileInput/PIRFileParser.cpp: In member function 'virtual void clustalw::PIRFileParser::getSecStructure(std::vector<char>&, std::vector<char>&, std::string&, int&, int)':
 clustalW/fileInput/PIRFileParser.cpp:292:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
   292 | void PIRFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
@@ -2540,10 +5083,6 @@
 clustalW/fileInput/PIRFileParser.cpp:293:86: warning: unused parameter 'length' [-Wunused-parameter]
   293 |                                     string& secStructName, int &structPenalties, int length)
       |                                                                                  ~~~~^~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o DebugLog.o clustalW/general/DebugLog.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o OutputFile.o clustalW/general/OutputFile.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Stats.o clustalW/general/Stats.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SymMatrix.o clustalW/general/SymMatrix.cpp
 In file included from clustalW/general/OutputFile.cpp:9:
 clustalW/general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
    26 |         std::auto_ptr<std::ofstream> file;
@@ -2556,6 +5095,22 @@
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UserParameters.o clustalW/general/UserParameters.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Utility.o clustalW/general/Utility.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o VectorOutOfRange.o clustalW/general/VectorOutOfRange.cpp
+clustalW/fileInput/RSFFileParser.cpp: In member function 'virtual void clustalw::RSFFileParser::getSecStructure(std::vector<char>&, std::vector<char>&, std::string&, int&, int)':
+clustalW/fileInput/RSFFileParser.cpp:240:51: warning: unused parameter 'gapPenaltyMask' [-Wunused-parameter]
+  240 | void RSFFileParser::getSecStructure(vector<char>& gapPenaltyMask, vector<char>& secStructMask,
+      |                                     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp
+In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/general/../alignment/Alignment.h:42,
+                 from clustalW/general/Stats.cpp:15:
+clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp
 clustalW/general/ClustalWResources.cpp: In member function 'std::string clustalw::ClustalWResources::findFile(std::string, clustalw::ClustalWResourcePathType) const':
 clustalW/general/ClustalWResources.cpp:106:12: warning: array subscript 1 is above array bounds of 'char [1]' [-Warray-bounds]
   106 |     delim[1] = 0;
@@ -2569,61 +5124,22 @@
 clustalW/general/ClustalWResources.cpp:104:10: note: destination object 'delim' of size 1
   104 |     char delim[1];
       |          ^~~~~
-In file included from clustalW/general/../alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/general/../alignment/Alignment.h:42,
-                 from clustalW/general/Stats.cpp:15:
-clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/general/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o CommandLineParser.o clustalW/interface/CommandLineParser.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o InteractiveMenu.o clustalW/interface/InteractiveMenu.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp
 clustalW/general/UserParameters.cpp: In constructor 'clustalw::UserParameters::UserParameters(bool)':
 clustalW/general/UserParameters.cpp:33:37: warning: unused parameter 'log' [-Wunused-parameter]
    33 | UserParameters::UserParameters(bool log)
       |                                ~~~~~^~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp
 clustalW/general/UserParameters.cpp: In member function 'int clustalw::UserParameters::resIndex(std::string, char)':
 clustalW/general/UserParameters.cpp:475:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
   475 |     register int i;
       |                  ^
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Iteration.o clustalW/multipleAlign/Iteration.cpp
-clustalW/general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)':
-clustalW/general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-   53 |     register int p;
-      |                  ^
-clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
-clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
-  251 |    int n;
-      |        ^
-clustalW/general/Utility.cpp: In member function 'virtual void clustalw::Utility::setInfoLabelPtr(QLabel*)':
-clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter]
-  519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj)
-      |                               ~~~~~~~~^~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o LowScoreSegProfile.o clustalW/multipleAlign/LowScoreSegProfile.cpp
-clustalW/general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)':
-clustalW/general/Utility.cpp:183:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  183 |         fgets(line, MAXLINE, stdin);
-      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~
-clustalW/general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)':
-clustalW/general/Utility.cpp:221:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  221 |         fgets(line, MAXLINE, stdin);
-      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o MSA.o clustalW/multipleAlign/MSA.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o MyersMillerProfileAlign.o clustalW/multipleAlign/MyersMillerProfileAlign.cpp
-In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/interface/../fileInput/../alignment/Alignment.h:42,
-                 from clustalW/interface/../fileInput/FileReader.h:12,
-                 from clustalW/interface/../Clustal.h:18,
-                 from clustalW/interface/InteractiveMenu.h:15,
-                 from clustalW/interface/InteractiveMenu.cpp:23:
-clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp
 In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/interface/../fileInput/../alignment/Alignment.h:42,
                  from clustalW/interface/../fileInput/FileReader.h:12,
@@ -2699,157 +5215,162 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   42 |         void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
-      |                                      ^~~~~~~~
+clustalW/general/Utility.cpp: In member function 'char* clustalw::Utility::rTrim(char*)':
+clustalW/general/Utility.cpp:53:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+   53 |     register int p;
+      |                  ^
+clustalW/general/Utility.cpp: In member function 'bool clustalw::Utility::lineType(char*, const char*)':
+clustalW/general/Utility.cpp:251:8: warning: variable 'n' set but not used [-Wunused-but-set-variable]
+  251 |    int n;
+      |        ^
+clustalW/general/Utility.cpp: In member function 'virtual void clustalw::Utility::setInfoLabelPtr(QLabel*)':
+clustalW/general/Utility.cpp:519:39: warning: unused parameter 'ptrToLabelObj' [-Wunused-parameter]
+  519 | void Utility::setInfoLabelPtr(QLabel* ptrToLabelObj)
+      |                               ~~~~~~~~^~~~~~~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp
+clustalW/general/Utility.cpp: In member function 'double clustalw::Utility::getReal(const char*, double, double, double)':
+clustalW/general/Utility.cpp:183:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  183 |         fgets(line, MAXLINE, stdin);
+      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~
+clustalW/general/Utility.cpp: In member function 'int clustalw::Utility::getInt(const char*, int, int, int)':
+clustalW/general/Utility.cpp:221:14: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  221 |         fgets(line, MAXLINE, stdin);
+      |         ~~~~~^~~~~~~~~~~~~~~~~~~~~~
+In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/multipleAlign/../alignment/Alignment.h:42,
+                 from clustalW/multipleAlign/Iteration.h:8,
+                 from clustalW/multipleAlign/Iteration.cpp:13:
+clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp
+In file included from clustalW/interface/../fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/interface/../fileInput/../alignment/Alignment.h:42,
+                 from clustalW/interface/../fileInput/FileReader.h:12,
+                 from clustalW/interface/../Clustal.h:18,
+                 from clustalW/interface/InteractiveMenu.h:15,
+                 from clustalW/interface/InteractiveMenu.cpp:23:
+clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/interface/../fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+In file included from clustalW/multipleAlign/Iteration.cpp:17:
+clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   38 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
+      |         ^~~~~~~~
 In file included from /usr/include/c++/12/memory:76,
-                 from clustalW/interface/../fileInput/FileReader.h:11:
+                 from clustalW/multipleAlign/../tree/TreeInterface.h:17:
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-In file included from clustalW/interface/../Clustal.h:20:
-clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   68 |         bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
-      |                               ^~~~~~~~
+clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   57 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
+      |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   69 |         string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
-      |                               ^~~~~~~~
+clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  102 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
+      |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   75 |         auto_ptr<ofstream> clustalOutFile;
+clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  108 |         auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   76 |         auto_ptr<ofstream> gcgOutFile;
+clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  133 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   77 |         auto_ptr<ofstream> nbrfOutFile;
+clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  138 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   78 |         auto_ptr<ofstream> phylipOutFile;
+clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  142 |         auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   79 |         auto_ptr<ofstream> gdeOutFile;
-      |         ^~~~~~~~
+clustalW/interface/../fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   42 |         void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser);
+      |                                      ^~~~~~~~
+In file included from /usr/include/c++/12/memory:76,
+                 from clustalW/interface/../fileInput/FileReader.h:11:
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   80 |         auto_ptr<ofstream> nexusOutFile;
-      |         ^~~~~~~~
+In file included from clustalW/interface/../Clustal.h:20:
+clustalW/interface/../alignment/AlignmentOutput.h:68:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   68 |         bool openExplicitFile(auto_ptr<ofstream>& outFile, string fileName);
+      |                               ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   81 |         auto_ptr<ofstream> fastaOutFile;
-      |         ^~~~~~~~
+clustalW/interface/../alignment/AlignmentOutput.h:69:31: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   69 |         string openOutputFile(auto_ptr<ofstream>& outFile, string prompt, string path,
+      |                               ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()':
-clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=]
-   41 |     catch(bad_alloc)
-      |           ^~~~~~~~~
-In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/multipleAlign/../alignment/Alignment.h:42,
-                 from clustalW/multipleAlign/Iteration.h:8,
-                 from clustalW/multipleAlign/Iteration.cpp:13:
-clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-In file included from clustalW/multipleAlign/Iteration.cpp:17:
-clustalW/multipleAlign/../tree/TreeInterface.h:38:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   38 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMat(vector<int>* seqWeights,
+clustalW/interface/../alignment/AlignmentOutput.h:75:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   75 |         auto_ptr<ofstream> clustalOutFile;
       |         ^~~~~~~~
-In file included from /usr/include/c++/12/memory:76,
-                 from clustalW/multipleAlign/../tree/TreeInterface.h:17:
+clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
+clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
+  170 |     int count;
+      |         ^~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/multipleAlign/../tree/TreeInterface.h:57:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   57 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTree(Alignment* alignPtr,
+clustalW/interface/../alignment/AlignmentOutput.h:76:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   76 |         auto_ptr<ofstream> gcgOutFile;
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/multipleAlign/../tree/TreeInterface.h:102:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  102 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatNJ(vector<int>* seqWeights,
+clustalW/interface/../alignment/AlignmentOutput.h:77:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   77 |         auto_ptr<ofstream> nbrfOutFile;
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/multipleAlign/../tree/TreeInterface.h:108:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  108 |         auto_ptr<AlignmentSteps> getWeightsAndStepsUseOldGuideTreeNJ(DistMatrix* distMat,
+clustalW/interface/../alignment/AlignmentOutput.h:78:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   78 |         auto_ptr<ofstream> phylipOutFile;
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/multipleAlign/../tree/TreeInterface.h:133:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  133 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromTreeNJ(Alignment* alignPtr,
+clustalW/interface/../alignment/AlignmentOutput.h:79:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   79 |         auto_ptr<ofstream> gdeOutFile;
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/multipleAlign/../tree/TreeInterface.h:138:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  138 |         auto_ptr<AlignmentSteps> getWeightsAndStepsFromDistMatUPGMA(vector<int>* seqWeights,
+clustalW/interface/../alignment/AlignmentOutput.h:80:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   80 |         auto_ptr<ofstream> nexusOutFile;
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/multipleAlign/../tree/TreeInterface.h:142:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  142 |         auto_ptr<AlignmentSteps> generateTreeFromDistMatUPGMA(RootedGuideTree* guideTree,
+clustalW/interface/../alignment/AlignmentOutput.h:81:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   81 |         auto_ptr<ofstream> fastaOutFile;
       |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/multipleAlign/Iteration.cpp: In member function 'bool clustalw::Iteration::removeFirstIterate(clustalw::Alignment*)':
-clustalW/multipleAlign/Iteration.cpp:170:9: warning: variable 'count' set but not used [-Wunused-but-set-variable]
-  170 |     int count;
-      |         ^~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileBase.o clustalW/multipleAlign/ProfileBase.cpp
-clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()':
-clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=]
-  520 |                 clustalObj->getHelp('C');
-      |                 ~~~~~~~~~~~~~~~~~~~^~~~~
-clustalW/interface/InteractiveMenu.cpp:521:13: note: here
-  521 |             case 'Q':
-      |             ^~~~
-clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()':
-clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
- 1190 |         system(lin1.c_str());
-      |         ~~~~~~^~~~~~~~~~~~~~
-In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/multipleAlign/../alignment/Alignment.h:42,
-                 from clustalW/multipleAlign/LowScoreSegProfile.h:13,
-                 from clustalW/multipleAlign/LowScoreSegProfile.cpp:9:
-clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
-  231 |                 tmpnam (buffer);
-      |                 ~~~~~~~^~~~~~~~
 In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/multipleAlign/../alignment/Alignment.h:42,
                  from clustalW/multipleAlign/ProfileBase.h:14,
@@ -2861,7 +5382,10 @@
 clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileStandard.o clustalW/multipleAlign/ProfileStandard.cpp
+clustalW/interface/InteractiveMenu.cpp: In constructor 'clustalw::InteractiveMenu::InteractiveMenu()':
+clustalW/interface/InteractiveMenu.cpp:41:11: warning: catching polymorphic type 'class std::bad_alloc' by value [-Wcatch-value=]
+   41 |     catch(bad_alloc)
+      |           ^~~~~~~~~
 clustalW/multipleAlign/MSA.cpp: In member function 'int clustalw::MSA::multiSeqAlign(clustalw::Alignment*, clustalw::DistMatrix*, std::vector<int>*, clustalw::AlignmentSteps*, int)':
 clustalW/multipleAlign/MSA.cpp:340:11: warning: unused variable 'alignmentScore' [-Wunused-variable]
   340 |       int alignmentScore = alnPtr->alignScore(); // ?? check, FS, 2009-05-18
@@ -2872,9 +5396,8 @@
       |                            ~~~~~~~^~~~~~~~~~
 In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/multipleAlign/../alignment/Alignment.h:42,
-                 from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10,
-                 from clustalW/multipleAlign/MyersMillerProfileAlign.h:10,
-                 from clustalW/multipleAlign/MyersMillerProfileAlign.cpp:10:
+                 from clustalW/multipleAlign/ProfileStandard.h:9,
+                 from clustalW/multipleAlign/ProfileStandard.cpp:9:
 clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
@@ -2891,43 +5414,63 @@
 clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ProfileWithSub.o clustalW/multipleAlign/ProfileWithSub.cpp
+In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/pairwise/../alignment/Alignment.h:42,
+                 from clustalW/pairwise/PairwiseAlignBase.h:10,
+                 from clustalW/pairwise/FastPairwiseAlign.h:9,
+                 from clustalW/pairwise/FastPairwiseAlign.cpp:10:
+clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
 In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/multipleAlign/../alignment/Alignment.h:42,
-                 from clustalW/multipleAlign/ProfileStandard.h:9,
-                 from clustalW/multipleAlign/ProfileStandard.cpp:9:
+                 from clustalW/multipleAlign/LowScoreSegProfile.h:13,
+                 from clustalW/multipleAlign/LowScoreSegProfile.cpp:9:
 clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FastPairwiseAlign.o clustalW/pairwise/FastPairwiseAlign.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o FullPairwiseAlign.o clustalW/pairwise/FullPairwiseAlign.cpp
 In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/multipleAlign/../alignment/Alignment.h:42,
-                 from clustalW/multipleAlign/ProfileWithSub.h:9,
-                 from clustalW/multipleAlign/ProfileWithSub.cpp:9:
+                 from clustalW/multipleAlign/ProfileAlignAlgorithm.h:10,
+                 from clustalW/multipleAlign/MyersMillerProfileAlign.h:10,
+                 from clustalW/multipleAlign/MyersMillerProfileAlign.cpp:10:
 clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o SubMatrix.o clustalW/substitutionMatrix/SubMatrix.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o AlignmentSteps.o clustalW/tree/AlignmentSteps.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp
-In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/pairwise/../alignment/Alignment.h:42,
-                 from clustalW/pairwise/PairwiseAlignBase.h:10,
-                 from clustalW/pairwise/FastPairwiseAlign.h:9,
-                 from clustalW/pairwise/FastPairwiseAlign.cpp:10:
-clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+In file included from clustalW/multipleAlign/../alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/multipleAlign/../alignment/Alignment.h:42,
+                 from clustalW/multipleAlign/ProfileWithSub.h:9,
+                 from clustalW/multipleAlign/ProfileWithSub.cpp:9:
+clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
-clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+clustalW/multipleAlign/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
+clustalW/multipleAlign/Iteration.cpp:231:24: warning: ignoring return value of 'char* tmpnam(char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+  231 |                 tmpnam (buffer);
+      |                 ~~~~~~~^~~~~~~~
+clustalW/interface/InteractiveMenu.cpp: In member function 'int clustalw::InteractiveMenu::secStrOutputOptions()':
+clustalW/interface/InteractiveMenu.cpp:520:36: warning: this statement may fall through [-Wimplicit-fallthrough=]
+  520 |                 clustalObj->getHelp('C');
+      |                 ~~~~~~~~~~~~~~~~~~~^~~~~
+clustalW/interface/InteractiveMenu.cpp:521:13: note: here
+  521 |             case 'Q':
+      |             ^~~~
+clustalW/interface/InteractiveMenu.cpp: In member function 'void clustalw::InteractiveMenu::doSystem()':
+clustalW/interface/InteractiveMenu.cpp:1190:15: warning: ignoring return value of 'int system(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
+ 1190 |         system(lin1.c_str());
+      |         ~~~~~~^~~~~~~~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTree.o clustalW/tree/ClusterTree.cpp
 In file included from clustalW/pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/pairwise/../alignment/Alignment.h:42,
                  from clustalW/pairwise/PairwiseAlignBase.h:10,
@@ -2939,35 +5482,6 @@
 clustalW/pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp
-In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/tree/../alignment/Alignment.h:42,
-                 from clustalW/tree/ClusterTree.h:20,
-                 from clustalW/tree/ClusterTree.cpp:9:
-clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-In file included from clustalW/tree/ClusterTree.h:23:
-clustalW/tree/../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   26 |         std::auto_ptr<std::ofstream> file;
-      |              ^~~~~~~~
-In file included from /usr/include/c++/12/memory:76,
-                 from clustalW/tree/ClusterTree.h:16:
-/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
-   64 |   template<typename> class auto_ptr;
-      |                            ^~~~~~~~
-clustalW/tree/ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   70 |         auto_ptr<clustalw::DistMatrix> quickDistMat;
-      |         ^~~~~~~~
-/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
-   64 |   template<typename> class auto_ptr;
-      |                            ^~~~~~~~
 In file included from clustalW/substitutionMatrix/SubMatrix.cpp:15:
 clustalW/substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
@@ -2975,14 +5489,8 @@
 clustalW/substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
-clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
-  580 |     int rs = 0, rl = 0;
-      |         ^~
-clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
-  580 |     int rs = 0, rl = 0;
-      |                 ^~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o ClusterTreeOutput.o clustalW/tree/ClusterTreeOutput.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o NJTree.o clustalW/tree/NJTree.cpp
 clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'void clustalw::SubMatrix::tempInterface(int, int)':
 clustalW/substitutionMatrix/SubMatrix.cpp:1613:35: warning: unused parameter 'alignResidueType' [-Wunused-parameter]
  1613 | void SubMatrix::tempInterface(int alignResidueType, int alignType)
@@ -2998,52 +5506,60 @@
 clustalW/substitutionMatrix/SubMatrix.cpp:1717:9: warning: variable 'maxRes' set but not used [-Wunused-but-set-variable]
  1717 |     int maxRes;
       |         ^~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RandomGenerator.o clustalW/tree/RandomGenerator.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Tree.o clustalW/tree/Tree.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o TreeInterface.o clustalW/tree/TreeInterface.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UnRootedClusterTree.o clustalW/tree/UnRootedClusterTree.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp
 In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/tree/../alignment/Alignment.h:42,
-                 from clustalW/tree/ClusterTreeOutput.h:11,
-                 from clustalW/tree/ClusterTreeOutput.cpp:9:
+                 from clustalW/tree/ClusterTree.h:20,
+                 from clustalW/tree/ClusterTree.cpp:9:
 clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-clustalW/tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)':
-clustalW/tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
-  164 |     register int i;
-      |                  ^
 In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/tree/../alignment/Alignment.h:42,
-                 from clustalW/tree/Tree.h:13,
-                 from clustalW/tree/Tree.cpp:10:
+                 from clustalW/tree/ClusterTreeOutput.h:11,
+                 from clustalW/tree/ClusterTreeOutput.cpp:9:
 clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-clustalW/tree/Tree.h:26:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   26 |         auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
-      |         ^~~~~~~~
+In file included from clustalW/tree/ClusterTree.h:23:
+clustalW/tree/../general/OutputFile.h:26:14: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   26 |         std::auto_ptr<std::ofstream> file;
+      |              ^~~~~~~~
 In file included from /usr/include/c++/12/memory:76,
-                 from clustalW/tree/Tree.h:15:
-/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
-   64 |   template<typename> class auto_ptr;
-      |                            ^~~~~~~~
-clustalW/tree/Tree.cpp:278:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  278 | auto_ptr<AlignmentSteps> Tree::createSets(int firstSeq, int lastSeq)
-      | ^~~~~~~~
+                 from clustalW/tree/ClusterTree.h:16:
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-clustalW/tree/Tree.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::Tree::createSets(int, int)':
-clustalW/tree/Tree.cpp:280:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-  280 |     auto_ptr<AlignmentSteps> progAlignSteps;
-      |     ^~~~~~~~
+clustalW/tree/ClusterTree.h:70:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   70 |         auto_ptr<clustalw::DistMatrix> quickDistMat;
+      |         ^~~~~~~~
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp
+clustalW/tree/ClusterTree.cpp: In member function 'void clustalw::ClusterTree::calcPercIdentity(std::ofstream*, clustalw::Alignment*)':
+clustalW/tree/ClusterTree.cpp:580:9: warning: variable 'rs' set but not used [-Wunused-but-set-variable]
+  580 |     int rs = 0, rl = 0;
+      |         ^~
+clustalW/tree/ClusterTree.cpp:580:17: warning: variable 'rl' set but not used [-Wunused-but-set-variable]
+  580 |     int rs = 0, rl = 0;
+      |                 ^~
+clustalW/tree/NJTree.cpp: In member function 'virtual void clustalw::NJTree::generateTree(clustalw::PhyloTree*, clustalw::DistMatrix*, clustalw::SeqInfo*, std::ofstream*)':
+clustalW/tree/NJTree.cpp:164:18: warning: ISO C++17 does not allow 'register' storage class specifier [-Wregister]
+  164 |     register int i;
+      |                  ^
 In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/tree/../alignment/Alignment.h:42,
                  from clustalW/tree/TreeInterface.h:19,
@@ -3208,6 +5724,41 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp
+In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/tree/../alignment/Alignment.h:42,
+                 from clustalW/tree/Tree.h:13,
+                 from clustalW/tree/Tree.cpp:10:
+clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/tree/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+g++ -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -dM -E -o moc_predefs.h /usr/lib/i386-linux-gnu/qt5/mkspecs/features/data/dummy.cpp
+/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp
+/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp
+clustalW/tree/Tree.h:26:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   26 |         auto_ptr<AlignmentSteps> createSets(int firstSeq, int lastSeq);
+      |         ^~~~~~~~
+In file included from /usr/include/c++/12/memory:76,
+                 from clustalW/tree/Tree.h:15:
+/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
+   64 |   template<typename> class auto_ptr;
+      |                            ^~~~~~~~
+clustalW/tree/Tree.cpp:278:1: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  278 | auto_ptr<AlignmentSteps> Tree::createSets(int firstSeq, int lastSeq)
+      | ^~~~~~~~
+/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
+   64 |   template<typename> class auto_ptr;
+      |                            ^~~~~~~~
+clustalW/tree/Tree.cpp: In member function 'std::auto_ptr<clustalw::AlignmentSteps> clustalw::Tree::createSets(int, int)':
+clustalW/tree/Tree.cpp:280:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+  280 |     auto_ptr<AlignmentSteps> progAlignSteps;
+      |     ^~~~~~~~
+/usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
+   64 |   template<typename> class auto_ptr;
+      |                            ^~~~~~~~
 In file included from clustalW/tree/../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/tree/../alignment/Alignment.h:42,
                  from clustalW/tree/ClusterTree.h:20,
@@ -3234,9 +5785,18 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o Node.o clustalW/tree/UPGMA/Node.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedClusterTree.o clustalW/tree/UPGMA/RootedClusterTree.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedGuideTree.o clustalW/tree/UPGMA/RootedGuideTree.cpp
+In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/tree/UPGMA/../../alignment/Alignment.h:42,
+                 from clustalW/tree/UPGMA/RootedGuideTree.h:17,
+                 from clustalW/tree/UPGMA/RootedGuideTree.cpp:10:
+clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp
+/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.cpp
 In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/tree/UPGMA/../../alignment/Alignment.h:42,
                  from clustalW/tree/UPGMA/../ClusterTree.h:20,
@@ -3269,7 +5829,6 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o RootedTreeOutput.o clustalW/tree/UPGMA/RootedTreeOutput.cpp
 In file included from clustalW/tree/UPGMA/RootedClusterTree.cpp:11:
 clustalW/tree/UPGMA/UPGMAAlgorithm.h:23:9: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
    23 |         auto_ptr<AlignmentSteps> generateTree(RootedGuideTree* phyTree,
@@ -3296,30 +5855,6 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o UPGMAAlgorithm.o clustalW/tree/UPGMA/UPGMAAlgorithm.cpp
-clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
-clustalW/substitutionMatrix/SubMatrix.cpp:1103:19: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
- 1103 |     return (maxRes);
-      |                   ^
-clustalW/substitutionMatrix/SubMatrix.cpp:998:9: note: 'n' was declared here
-  998 |     int n, llimit, ulimit;
-      |         ^
-In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/tree/UPGMA/../../alignment/Alignment.h:42,
-                 from clustalW/tree/UPGMA/RootedGuideTree.h:17,
-                 from clustalW/tree/UPGMA/RootedGuideTree.cpp:10:
-clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-g++ -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -dM -E -o moc_predefs.h /usr/lib/i386-linux-gnu/qt5/mkspecs/features/data/dummy.cpp
-/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentFormatOptions.h -o moc_AlignmentFormatOptions.cpp
-/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentParameters.h -o moc_AlignmentParameters.cpp
-/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentViewerWidget.h -o moc_AlignmentViewerWidget.cpp
-/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignmentWidget.h -o moc_AlignmentWidget.cpp
-/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp
 In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/tree/UPGMA/../../alignment/Alignment.h:42,
                  from clustalW/tree/UPGMA/RootedGuideTree.h:17,
@@ -3331,9 +5866,8 @@
 clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
+/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include AlignOutputFileNames.h -o moc_AlignOutputFileNames.cpp
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include BootstrapTreeDialog.h -o moc_BootstrapTreeDialog.cpp
-/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp
-/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include ColumnScoreParams.h -o moc_ColumnScoreParams.cpp
 In file included from clustalW/tree/UPGMA/../../alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/tree/UPGMA/../../alignment/Alignment.h:42,
                  from clustalW/tree/UPGMA/RootedGuideTree.h:17,
@@ -3365,12 +5899,21 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
+/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include ColorFileXmlParser.h -o moc_ColorFileXmlParser.cpp
+/usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include ColumnScoreParams.h -o moc_ColumnScoreParams.cpp
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include FileDialog.h -o moc_FileDialog.cpp
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include HelpDisplayWidget.h -o moc_HelpDisplayWidget.cpp
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include HistogramWidget.h -o moc_HistogramWidget.cpp
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include LowScoringSegParams.h -o moc_LowScoringSegParams.cpp
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include mainwindow.h -o moc_mainwindow.cpp
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include PairwiseParams.h -o moc_PairwiseParams.cpp
+clustalW/substitutionMatrix/SubMatrix.cpp: In member function 'int clustalw::SubMatrix::readMatrixSeries(const char*, clustalw::Matrix&, clustalw::Xref&)':
+clustalW/substitutionMatrix/SubMatrix.cpp:1103:19: warning: 'n' may be used uninitialized [-Wmaybe-uninitialized]
+ 1103 |     return (maxRes);
+      |                   ^
+clustalW/substitutionMatrix/SubMatrix.cpp:998:9: note: 'n' was declared here
+  998 |     int n, llimit, ulimit;
+      |         ^
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include ProteinGapParameters.h -o moc_ProteinGapParameters.cpp
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include PSPrinter.h -o moc_PSPrinter.cpp
 /usr/lib/qt5/bin/moc -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB --include /build/clustalx-2.1+lgpl/moc_predefs.h -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl -I/build/clustalx-2.1+lgpl/clustalW/general -I/build/clustalx-2.1+lgpl/clustalW/substitutionMatrix -I/build/clustalx-2.1+lgpl/clustalW/alignment -I/build/clustalx-2.1+lgpl/clustalW -I/build/clustalx-2.1+lgpl/clustalW/fileInput -I/build/clustalx-2.1+lgpl/clustalW/interface -I/build/clustalx-2.1+lgpl/clustalW/pairwise -I/build/clustalx-2.1+lgpl/clustalW/multipleAlign -I/build/clustalx-2.1+lgpl/clustalW/tree -I/build/clustalx-2.1+lgpl/clustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I/usr/include/c++/12 -I/usr/include/i386-linux-gnu/c++/12 -I/usr/include/c++/12/backward -I/usr/lib/gcc/i686-linux-gnu/12/include -I/usr/local/include -I/usr/include/i386-linux-gnu -I/usr/include SaveSeqFile.h -o moc_SaveSeqFile.cpp
@@ -3388,6 +5931,12 @@
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_BootstrapTreeDialog.o moc_BootstrapTreeDialog.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColorFileXmlParser.o moc_ColorFileXmlParser.cpp
 g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ColumnScoreParams.o moc_ColumnScoreParams.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from AlignmentViewerWidget.h:36,
@@ -3401,6 +5950,19 @@
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
+                 from HelpDisplayWidget.h:18,
+                 from moc_HelpDisplayWidget.cpp:10:
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
+      |                                                              ^~~~~~~~~~~~~~
+clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
+   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
+      |                                                                  ^~~~~~~~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp
+In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
+                 from clustalW/alignment/Alignment.h:42,
+                 from ClustalQtParams.h:13,
                  from AlignOutputFileNames.h:10,
                  from moc_AlignOutputFileNames.cpp:10:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
@@ -3417,9 +5979,7 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_FileDialog.o moc_FileDialog.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HelpDisplayWidget.o moc_HelpDisplayWidget.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_HistogramWidget.o moc_HistogramWidget.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from AlignmentWidget.h:41,
@@ -3430,7 +5990,9 @@
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_LowScoringSegParams.o moc_LowScoringSegParams.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
@@ -3450,49 +6012,33 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp
+g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
-                 from ClustalQtParams.h:13,
-                 from HardCodedColorScheme.h:8,
-                 from ColorParameters.h:11,
-                 from ColorFileXmlParser.h:9,
-                 from moc_ColorFileXmlParser.cpp:10:
+                 from AlignmentViewerWidget.h:36,
+                 from mainwindow.h:37,
+                 from moc_mainwindow.cpp:10:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_mainwindow.o moc_mainwindow.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PairwiseParams.o moc_PairwiseParams.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_ProteinGapParameters.o moc_ProteinGapParameters.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_PSPrinter.o moc_PSPrinter.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SaveSeqFile.o moc_SaveSeqFile.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
-                 from HelpDisplayWidget.h:18,
-                 from moc_HelpDisplayWidget.cpp:10:
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
-      |                                                              ^~~~~~~~~~~~~~
-clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
-   97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
-      |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SearchForString.o moc_SearchForString.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SecStructOptions.o moc_SecStructOptions.cpp
-In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
-                 from clustalW/alignment/Alignment.h:42,
-                 from AlignmentViewerWidget.h:36,
-                 from mainwindow.h:37,
-                 from moc_mainwindow.cpp:10:
+                 from HardCodedColorScheme.h:8,
+                 from ColorParameters.h:11,
+                 from ColorFileXmlParser.h:9,
+                 from moc_ColorFileXmlParser.cpp:10:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_SeqNameWidget.o moc_SeqNameWidget.cpp
 In file included from clustalW/Clustal.h:18,
                  from mainwindow.h:45:
 clustalW/fileInput/FileReader.h:42:38: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
@@ -3558,7 +6104,6 @@
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeFormatOptions.o moc_TreeFormatOptions.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
@@ -3572,8 +6117,6 @@
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_TreeOutputFileNames.o moc_TreeOutputFileNames.cpp
-g++ -c -pipe -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wextra -D_REENTRANT -fPIC -DOS_UNIX -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_GUI_LIB -DQT_XML_LIB -DQT_CORE_LIB -g -O2 -ffile-prefix-map=/build/clustalx-2.1+lgpl=. -fstack-protector-strong -Wformat -Werror=format-security -I. -I. -IclustalW/general -IclustalW/substitutionMatrix -IclustalW/alignment -IclustalW -IclustalW/fileInput -IclustalW/interface -IclustalW/pairwise -IclustalW/multipleAlign -IclustalW/tree -IclustalW/tree/UPGMA -I/usr/include/i386-linux-gnu/qt5 -I/usr/include/i386-linux-gnu/qt5/QtWidgets -I/usr/include/i386-linux-gnu/qt5/QtGui -I/usr/include/i386-linux-gnu/qt5/QtXml -I/usr/include/i386-linux-gnu/qt5/QtCore -I. -I/usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -o moc_WritePostscriptFile.o moc_WritePostscriptFile.cpp
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
@@ -3598,38 +6141,38 @@
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
-                 from TreeOutputFileNames.h:10,
-                 from moc_TreeOutputFileNames.cpp:10:
+                 from WritePostscriptFile.h:10,
+                 from moc_WritePostscriptFile.cpp:10:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-TreeOutputFileNames.h:73:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   73 |     auto_ptr<clustalw::TreeNames> treeFileNames;
+WritePostscriptFile.h:88:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   88 |     auto_ptr<PostscriptFileParams> params;
       |     ^~~~~~~~
 In file included from /usr/include/c++/12/memory:76,
-                 from moc_TreeOutputFileNames.cpp:9:
+                 from moc_WritePostscriptFile.cpp:9:
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
 In file included from clustalW/alignment/../substitutionMatrix/globalmatrix.h:8,
                  from clustalW/alignment/Alignment.h:42,
                  from ClustalQtParams.h:13,
-                 from WritePostscriptFile.h:10,
-                 from moc_WritePostscriptFile.cpp:10:
+                 from TreeOutputFileNames.h:10,
+                 from moc_TreeOutputFileNames.cpp:10:
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    96 |         void printInFormat(vector<short>& temp, char* name = "tempfile.out");
       |                                                              ^~~~~~~~~~~~~~
 clustalW/alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings]
    97 |         void printVectorToFile(vector<short>& temp, char* name = "tempfile.out");
       |                                                                  ^~~~~~~~~~~~~~
-WritePostscriptFile.h:88:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
-   88 |     auto_ptr<PostscriptFileParams> params;
+TreeOutputFileNames.h:73:5: warning: 'template<class> class std::auto_ptr' is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations]
+   73 |     auto_ptr<clustalw::TreeNames> treeFileNames;
       |     ^~~~~~~~
 In file included from /usr/include/c++/12/memory:76,
-                 from moc_WritePostscriptFile.cpp:9:
+                 from moc_TreeOutputFileNames.cpp:9:
 /usr/include/c++/12/bits/unique_ptr.h:64:28: note: declared here
    64 |   template<typename> class auto_ptr;
       |                            ^~~~~~~~
@@ -3672,12 +6215,14 @@
 dpkg-buildpackage: info: binary-only upload (no source included)
 dpkg-genchanges: info: not including original source code in upload
 I: copying local configuration
+I: user script /srv/workspace/pbuilder/93232/tmp/hooks/B01_cleanup starting
+I: user script /srv/workspace/pbuilder/93232/tmp/hooks/B01_cleanup finished
 I: unmounting dev/ptmx filesystem
 I: unmounting dev/pts filesystem
 I: unmounting dev/shm filesystem
 I: unmounting proc filesystem
 I: unmounting sys filesystem
 I: cleaning the build env 
-I: removing directory /srv/workspace/pbuilder/26567 and its subdirectories
-I: Current time: Mon Jun 12 09:41:39 -12 2023
-I: pbuilder-time-stamp: 1686606099
+I: removing directory /srv/workspace/pbuilder/93232 and its subdirectories
+I: Current time: Mon Jul 15 18:06:00 +14 2024
+I: pbuilder-time-stamp: 1721016360