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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/quicktree">Debian Med / quicktree</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/quicktree/-/commit/a3fc7a1c9133243d494b7485d4e01e4bcbb1045a">a3fc7a1c</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-17T12:21:33+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Libsonlib and signalalign need more care first before we go this hackish route
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<h4>2 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/quicktree/-/commit/a3fc7a1c9133243d494b7485d4e01e4bcbb1045a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,8 @@ quicktree (2.5-3) UNRELEASED; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * To enable removing quicktree source code copy from libsonlib package</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> a static library is created here</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> FIXME: The above is deactivated. Libsonlib and signalalign need more</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> care first before we go this hackish route</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 16 Jun 2020 09:35:08 +0200</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/quicktree/-/commit/a3fc7a1c9133243d494b7485d4e01e4bcbb1045a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,25 +31,26 @@ Description: Neighbor-Joining algorithm for phylogenies</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> The tress are written to stdout, in the Newick/New-Hampshire format</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> use by PHYLIP and many other programs</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">Package: libquicktree-dev</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="plaintext">Description: Neighbor-Joining algorithm for phylogenies (development)</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="plaintext"> QuickTree is an efficient implementation of the Neighbor-Joining</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext"> algorithm (PMID: 3447015), capable of reconstructing phylogenies from</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="plaintext"> huge alignments in time less than the age of the universe.</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="plaintext"> QuickTree accepts both distance matrix and multiple-sequence-aligment</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext"> inputs. The former should be in PHYLIP format. The latter should be</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext"> in Stockholm format, which is the native alignment format for the Pfam</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="plaintext"> database. Alignments in various formats can be converted to Stockholm</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> format with the sreformat program, which is part of the HMMer package</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="plaintext"> (hmmer.org).</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="plaintext"> The tress are written to stdout, in the Newick/New-Hampshire format</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="plaintext"> use by PHYLIP and many other programs</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext"> This package contains some header files from quicktree that are used</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext"> by other packages.</span></pre>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">#FIXME: This is needed for libsonlib as predependency of signalalign - but things need to be clarified first</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">#Package: libquicktree-dev</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">#Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">#Section: libdevel</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">#Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"># ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">#Description: Neighbor-Joining algorithm for phylogenies (development)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"># QuickTree is an efficient implementation of the Neighbor-Joining</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"># algorithm (PMID: 3447015), capable of reconstructing phylogenies from</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"># huge alignments in time less than the age of the universe.</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"># .</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"># QuickTree accepts both distance matrix and multiple-sequence-aligment</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"># inputs. The former should be in PHYLIP format. The latter should be</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"># in Stockholm format, which is the native alignment format for the Pfam</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"># database. Alignments in various formats can be converted to Stockholm</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"># format with the sreformat program, which is part of the HMMer package</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"># (hmmer.org).</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"># .</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"># The tress are written to stdout, in the Newick/New-Hampshire format</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"># use by PHYLIP and many other programs</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"># .</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"># This package contains some header files from quicktree that are used</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"># by other packages.</span></pre>
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