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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/terraphast">Debian Med / terraphast</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/terraphast/-/commit/b730cc401c9daaba8bbbc329ddb627ab0019647d">b730cc40</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2021-10-22T10:01:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add publication
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/terraphast/-/commit/1f3d828389abd7fea64526afb32a3e40ef5f9dda">1f3d8283</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-10-22T10:22:06+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Override dh_install
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#dc51acfe4028828dad214325ef76005d4972ac66">
<span class="new-file">
+
debian/libterraphast-dev.install
</span>
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</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#515952116c3d757fd2f5ac6241b0e6c72cae28a7">
<span class="new-file">
+
debian/terraphast.install
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<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<span class="new-file">
+
debian/upstream/metadata
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</a>
</li>
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<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/terraphast/-/compare/e6eb13ab8a5bcf1ae688c73b08f8a15448d3c658...1f3d828389abd7fea64526afb32a3e40ef5f9dda#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Section: science</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> cmake,</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> d<span class="idiff left right">-shlibs</span>,</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> d<span class="idiff left right">h-exec</span>,</span>
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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libgmp3-dev</span>
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<td class="old_line diff-line-num" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">Standards-Version: 4.6.0</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/terraphast</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,3 +25,19 @@ Description: enumerate terraces in phylogenetic tree space</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> Program output states some imput data properties, the species whose leaf</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> edge is used as a new tree root, and the resulting supertree in</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> compressed newick format.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Package: libterraphast-dev</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">Architecture: any</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Section: libdevel</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Depends: ${shlibs:Depends},</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> ${misc:Depends}</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">Description: enumerate terraces in phylogenetic tree space (development lib)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> Terraphast takes a .nkw file in Newick format and a genes/sites file,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> which denotes whether (1) or not (0) gene i is present in species j.</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> Program output states some imput data properties, the species whose leaf</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> edge is used as a new tree root, and the resulting supertree in</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> compressed newick format.</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> This package contains a library to use the terraphast algorithm in own</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> projects.</span></pre>
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<a href="https://salsa.debian.org/med-team/terraphast/-/compare/e6eb13ab8a5bcf1ae688c73b08f8a15448d3c658...1f3d828389abd7fea64526afb32a3e40ef5f9dda#dc51acfe4028828dad214325ef76005d4972ac66"><strong>debian/libterraphast-dev.install</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/dh-exec</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">-*/*.</span><span class="n" style="color: #333;">a</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">$</span><span class="p">{</span><span class="no" style="color: #008080;">DEB_HOST_MULTIARCH</span><span class="p">}</span><span class="o" style="font-weight: 600;">/</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="k" style="font-weight: 600;">include</span> <span class="n" style="color: #333;">usr</span></span></pre>
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<a href="https://salsa.debian.org/med-team/terraphast/-/compare/e6eb13ab8a5bcf1ae688c73b08f8a15448d3c658...1f3d828389abd7fea64526afb32a3e40ef5f9dda#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -2,9 +2,15 @@</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"># DH_VERBOSE := 1</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">include /usr/share/dpkg/default.mk</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"># for hardening you might like to uncomment this:</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"># export DEB_BUILD_MAINT_OPTIONS=hardening=+all</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> dh $@</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> mkdir -p debian/$(DEB_SOURCE)/usr/bin</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> mv obj-$$(dpkg-architecture -qDEB_TARGET_GNU_TYPE)/app debian/$(DEB_SOURCE)/usr/bin/$(DEB_SOURCE)</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> dh_install</span></pre>
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<a href="https://salsa.debian.org/med-team/terraphast/-/compare/e6eb13ab8a5bcf1ae688c73b08f8a15448d3c658...1f3d828389abd7fea64526afb32a3e40ef5f9dda#515952116c3d757fd2f5ac6241b0e6c72cae28a7"><strong>debian/terraphast.install</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="php"><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">-*/</span><span class="n" style="color: #333;">isomorphic</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">terraphast</span><span class="o" style="font-weight: 600;">/</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="php"><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">-*/</span><span class="n" style="color: #333;">nwk_to_dot</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">terraphast</span><span class="o" style="font-weight: 600;">/</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="php"><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">-*/</span><span class="n" style="color: #333;">reroot</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">terraphast</span><span class="o" style="font-weight: 600;">/</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="php"><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">-*/</span><span class="n" style="color: #333;">site_gen</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">terraphast</span><span class="o" style="font-weight: 600;">/</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="php"><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">-*/</span><span class="n" style="color: #333;">tree_gen</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">terraphast</span><span class="o" style="font-weight: 600;">/</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="php"><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">-*/</span><span class="n" style="color: #333;">validated_run</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">terraphast</span><span class="o" style="font-weight: 600;">/</span></span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="php"><span class="n" style="color: #333;">obj</span><span class="o" style="font-weight: 600;">-*/</span><span class="n" style="color: #333;">verbose_run</span> <span class="n" style="color: #333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">lib</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">terraphast</span><span class="o" style="font-weight: 600;">/</span></span></pre>
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<a href="https://salsa.debian.org/med-team/terraphast/-/compare/e6eb13ab8a5bcf1ae688c73b08f8a15448d3c658...1f3d828389abd7fea64526afb32a3e40ef5f9dda#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Reference:</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"> - Author: Michael J. Sanderson and Michelle M. McMahon and Mike Steel</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> Title: Terraces in phylogenetic tree space</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> Journal: Science</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Year: 2011</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> Volume: 333</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> Number: 6041</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Pages: 448-450</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> DOI: 10.1126/science.1206357</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> PMID: 21680810</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> URL: https://www.science.org/doi/10.1126/science.1206357</span></pre>
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