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1 ·5e9366fd9b85eb8f73e5f0d233497ee4·696544·doc·optional·python-cogent-doc_2020.12.21a+dfsg-4+deb11u1_all.deb1 ·264e2141b6242438c2044f99d0f0161d·696488·doc·optional·python-cogent-doc_2020.12.21a+dfsg-4+deb11u1_all.deb
2 ·c353bae6ea5be90601a60118ae62f38d·1366496·python·optional·python3-cogent3_2020.12.21a+dfsg-4+deb11u1_armhf.deb2 ·c353bae6ea5be90601a60118ae62f38d·1366496·python·optional·python3-cogent3_2020.12.21a+dfsg-4+deb11u1_armhf.deb
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347 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-12-13·11:30:00.000000·./usr/share/doc/python-cogent-doc/html/api/table/347 drwxr-xr-x···0·root·········(0)·root·········(0)········0·2023-12-13·11:30:00.000000·./usr/share/doc/python-cogent-doc/html/api/table/
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349 -rw-r--r--···0·root·········(0)·root·········(0)····13340·2023-12-13·11:30:00.000000·./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Columns.html349 -rw-r--r--···0·root·········(0)·root·········(0)····13340·2023-12-13·11:30:00.000000·./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Columns.html
350 -rw-r--r--···0·root·········(0)·root·········(0)····49787·2023-12-13·11:30:00.000000·./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Table.html350 -rw-r--r--···0·root·········(0)·root·········(0)····49787·2023-12-13·11:30:00.000000·./usr/share/doc/python-cogent-doc/html/api/table/classes/cogent3.util.table.Table.html
351 -rw-r--r--···0·root·········(0)·root·········(0)·····6823·2023-12-13·11:30:00.000000·./usr/share/doc/python-cogent-doc/html/api/table/table.html351 -rw-r--r--···0·root·········(0)·root·········(0)·····6823·2023-12-13·11:30:00.000000·./usr/share/doc/python-cogent-doc/html/api/table/table.html
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./usr/share/doc/python-cogent-doc/html/api/tree/classes/cogent3.core.tree.PhyloNode.html
'html2text' not available in path. Installing the 'html2text' package may produce better output.
    
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186 <p>Note:·names·present·in·only·one·of·the·two·trees·will·count·as186 <p>Note:·names·present·in·only·one·of·the·two·trees·will·count·as
187 mismatches:·if·you·don’t·want·this·behavior,·strip·out·the·non-matching187 mismatches:·if·you·don’t·want·this·behavior,·strip·out·the·non-matching
188 tips·first.</p>188 tips·first.</p>
189 </dd></dl>189 </dd></dl>
  
190 <dl·class="py·method">190 <dl·class="py·method">
191 <dt·id="cogent3.core.tree.PhyloNode.compare_by_tip_distances">191 <dt·id="cogent3.core.tree.PhyloNode.compare_by_tip_distances">
192 <code·class="sig-name·descname">compare_by_tip_distances</code><span·class="sig-paren">(</span><em·class="sig-param">other</em>,·<em·class="sig-param">sample=None</em>,·<em·class="sig-param">dist_f=&lt;function·distance_from_r&gt;</em>,·<em·class="sig-param">shuffle_f=&lt;bound·method·Random.shuffle·of·&lt;random.Random·object·at·0xa86de0&gt;&gt;</em><span·class="sig-paren">)</span><a·class="headerlink"·href="#cogent3.core.tree.PhyloNode.compare_by_tip_distances"·title="Permalink·to·this·definition">¶</a></dt>192 <code·class="sig-name·descname">compare_by_tip_distances</code><span·class="sig-paren">(</span><em·class="sig-param">other</em>,·<em·class="sig-param">sample=None</em>,·<em·class="sig-param">dist_f=&lt;function·distance_from_r&gt;</em>,·<em·class="sig-param">shuffle_f=&lt;bound·method·Random.shuffle·of·&lt;random.Random·object·at·0x1cf5590&gt;&gt;</em><span·class="sig-paren">)</span><a·class="headerlink"·href="#cogent3.core.tree.PhyloNode.compare_by_tip_distances"·title="Permalink·to·this·definition">¶</a></dt>
193 <dd><p>Compares·self·to·other·using·tip-to-tip·distance·matrices.</p>193 <dd><p>Compares·self·to·other·using·tip-to-tip·distance·matrices.</p>
194 <p>Value·returned·is·dist_f(m1,·m2)·for·the·two·matrices.·Default·is194 <p>Value·returned·is·dist_f(m1,·m2)·for·the·two·matrices.·Default·is
195 to·use·the·Pearson·correlation·coefficient,·with·+1·giving·a·distance195 to·use·the·Pearson·correlation·coefficient,·with·+1·giving·a·distance
196 of·0·and·-1·giving·a·distance·of·+1·(the·madimum·possible·value).196 of·0·and·-1·giving·a·distance·of·+1·(the·madimum·possible·value).
197 Depending·on·the·application,·you·might·instead·want·to·use197 Depending·on·the·application,·you·might·instead·want·to·use
198 distance_from_r_squared,·which·counts·correlations·of·both·+1·and·-1198 distance_from_r_squared,·which·counts·correlations·of·both·+1·and·-1
199 as·identical·(0·distance).</p>199 as·identical·(0·distance).</p>
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830 ········"2":·"py:method",830 ········"2":·"py:method",
831 ········"3":·"py:attribute",831 ········"3":·"py:attribute",
832 ········"4":·"py:exception"832 ········"4":·"py:exception"
833 ····},833 ····},
834 ····terms:·{834 ····terms:·{
835 ········"0015588630350439783":·93,835 ········"0015588630350439783":·93,
836 ········"005":·[16,·17],836 ········"005":·[16,·17],
837 ········"0xa86de0":·33,837 ········"0x1cf5590":·33,
838 ········"100":·[7,·12,·16,·17,·18,·31,·33,·60,·64],838 ········"100":·[7,·12,·16,·17,·18,·31,·33,·60,·64],
839 ········"1000":·99,839 ········"1000":·99,
840 ········"1978":·86,840 ········"1978":·86,
841 ········"1981":·99,841 ········"1981":·99,
842 ········"1987":·42,842 ········"1987":·42,
843 ········"1992":·66,843 ········"1992":·66,
844 ········"1994":·[83,·90],844 ········"1994":·[83,·90],
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