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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/iqtree">Debian Med / iqtree</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/commit/4230ace901096d9d5f1aee4fbba20cac86a72037">4230ace9</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-04T12:52:47Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/commit/8f5b82892034ac28f35281b47a218cc52322ad91">8f5b8289</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-04T12:52:48Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.6.12+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/commit/43230e6e3bf0bc6067f200c68ca5cf90ea984d98">43230e6e</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-04T12:52:52Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.6.12+dfsg'
Update to upstream version '1.6.12+dfsg'
with Debian dir e98239462030d10023bdbf8b5c3422a6b29dbcba</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/commit/42926f8818c3e1ba56a595051e53e2d242594070">42926f88</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-04T12:52:54Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/iqtree/commit/f24fc79b601ae043ff5247d5ce3cd7f18e00824b">f24fc79b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-04T13:13:31Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version - upload
</pre>
</li>
</ul>
<h4>11 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
</a>
</li>
<li class="file-stats">
<a href="#b41319330232826b2116256a2de6d4ea1651747d">
alignment/alignment.cpp
</a>
</li>
<li class="file-stats">
<a href="#c95968f7f55e25ff0d517f88aacae0ecd72a8e70">
alignment/alignmentpairwise.cpp
</a>
</li>
<li class="file-stats">
<a href="#1d1fdc052f5fcf9ab26c74024f124949c4236777">
alignment/superalignment.cpp
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#a7ac8f866fa5767febd882507b49374354178d30">
main/phyloanalysis.cpp
</a>
</li>
<li class="file-stats">
<a href="#182d27852fc1f61eed93e31783224a351bfaea3c">
main/phylotesting.cpp
</a>
</li>
<li class="file-stats">
<a href="#f239d8758cbcf834f3f5227bb6a482150c6d1695">
tree/mtree.cpp
</a>
</li>
<li class="file-stats">
<a href="#eb644fdc89c64d146a52d5305e863af83a4f64ab">
tree/mtreeset.cpp
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/iqtree/compare/2c73dfd20694ecad26fd3de621af6dfaf34d3ae5...f24fc79b601ae043ff5247d5ce3cd7f18e00824b#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="51" 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="51" 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">@@ -51,7 +51,7 @@ add_definitions(-DIQ_TREE)</td>
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<td class="diff-line-num old_line" data-linenumber="51" 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">
51
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<td class="diff-line-num new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># The version number.</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="52" 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">
52
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<td class="diff-line-num new_line" data-linenumber="52" 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="LC52" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>iqtree_VERSION_MAJOR 1<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="53" 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">
53
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<td class="diff-line-num new_line" data-linenumber="53" 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">
53
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>iqtree_VERSION_MINOR 6<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
54
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<td class="diff-line-num new_line old" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>iqtree_VERSION_PATCH <span class="s2" style="color: #d14;">"1<span class="idiff left right">1</span>"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span> <span class="p">(</span>iqtree_VERSION_PATCH <span class="s2" style="color: #d14;">"1<span class="idiff left right">2</span>"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="55" 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">
55
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<td class="diff-line-num new_line" data-linenumber="55" 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">
55
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cmake"></span>
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<td class="diff-line-num old_line" data-linenumber="56" 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">
56
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<td class="diff-line-num new_line" data-linenumber="56" 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">
56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>BUILD_SHARED_LIBS OFF<span class="p">)</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="57" 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">
57
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<td class="diff-line-num new_line" data-linenumber="57" 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">
57
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC57" class="line" lang="cmake"></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="277" 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="277" 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">@@ -277,10 +277,10 @@ if (NOT IQTREE_FLAGS MATCHES "single")</td>
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<td class="diff-line-num old_line" data-linenumber="277" 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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<td class="diff-line-num new_line" data-linenumber="277" 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="LC277" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_C_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_C_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -pthread"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -fopenmp -pthread"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="279" 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">
279
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<td class="diff-line-num new_line" data-linenumber="279" 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="LC279" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">elseif</span> <span class="p">(</span>CLANG<span class="p">)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="diff-line-num new_line old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>APPLE<span class="p">)</span></span>
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<td class="diff-line-num new old_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">if</span> <span class="p">(</span>APPLE<span class="idiff left right"> OR WIN32</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="281" 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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<td class="diff-line-num new_line" data-linenumber="281" 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="LC281" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_C_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_C_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -pthread"</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -Xpreprocessor -fopenmp -pthread"</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="idiff">CMAKE_EXE_LINKER_FLAGS </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">CMAKE_EXE_LINKER_FLAGS</span></span><span class="si" style="color: #d14;"><span class="idiff">}</span></span><span class="s2" style="color: #d14;"><span class="idiff right"> -Xpreprocessor -fopenmp</span> -lomp"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p"><span class="idiff left">(</span></span><span class="idiff">CMAKE_EXE_LINKER_FLAGS </span><span class="s2" style="color: #d14;"><span class="idiff">"</span></span><span class="si" style="color: #d14;"><span class="idiff">${</span></span><span class="nv" style="color: #008080;"><span class="idiff">CMAKE_EXE_LINKER_FLAGS</span></span><span class="si" style="color: #d14;"><span class="idiff right">}</span></span><span class="s2" style="color: #d14;"> -lomp"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">else</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_C_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_C_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -pthread"</span><span class="p">)</span></span>
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cmake"> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>CMAKE_CXX_FLAGS <span class="s2" style="color: #d14;">"</span><span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_CXX_FLAGS</span><span class="si" style="color: #d14;">}</span><span class="s2" style="color: #d14;"> -fopenmp -pthread"</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/iqtree/compare/2c73dfd20694ecad26fd3de621af6dfaf34d3ae5...f24fc79b601ae043ff5247d5ce3cd7f18e00824b#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">IQ-TREE</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=======</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Github All Releases</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/github/downloads/Cibiv/IQ-TREE/total.svg?style=social&logo=github&label=Download</span><span class="p">)</span>](https://github.com/Cibiv/IQ-TREE/releases)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![BioConda downloads</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/iqtree.svg?style=flag&label=BioConda%20install</span><span class="p">)</span>](https://anaconda.org/bioconda/iqtree)</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/bqminh/IQ-TREE.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/bqminh/IQ-TREE)</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![License: GPL v2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v2-blue.svg</span><span class="p">)</span>](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<a href="https://salsa.debian.org/med-team/iqtree/compare/2c73dfd20694ecad26fd3de621af6dfaf34d3ae5...f24fc79b601ae043ff5247d5ce3cd7f18e00824b#b41319330232826b2116256a2de6d4ea1651747d"><strong>alignment/alignment.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="312" 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>
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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">@@ -312,7 +312,7 @@ Alignment *Alignment::removeIdenticalSeq(string not_remove, bool keep_two, StrVe</td>
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<pre style="margin: 0;"> <span id="LC312" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">checked</span><span class="p">[</span><span class="n" style="color: #333;">seq1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC313" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">first_ident_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">getNSeq</span><span class="p">();</span> <span class="n" style="color: #333;">seq2</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old old_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getSeqName</span><span class="p">(</span><span class="n" style="color: #333;">seq2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">not_remove</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getSeqName</span><span class="p">(</span><span class="n" style="color: #333;">seq2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">not_remove</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">removed</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">seq2</span></span><span class="p"><span class="idiff right">]</span>)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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316
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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">equal_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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317
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317
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<pre style="margin: 0;"> <span id="LC317" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begin</span><span class="p">();</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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318
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318
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">)[</span><span class="n" style="color: #333;">seq1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">it</span><span class="p">)[</span><span class="n" style="color: #333;">seq2</span><span class="p">])</span> <span class="p">{</span></span>
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<a href="https://salsa.debian.org/med-team/iqtree/compare/2c73dfd20694ecad26fd3de621af6dfaf34d3ae5...f24fc79b601ae043ff5247d5ce3cd7f18e00824b#c95968f7f55e25ff0d517f88aacae0ecd72a8e70"><strong>alignment/alignmentpairwise.cpp</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">@@ -259,17 +259,26 @@ void AlignmentPairwise::computeFuncDerv(double value, double &df, double &ddf) {</td>
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259
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"></span>
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260
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260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">cat</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">cat</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">ncat</span><span class="p">;</span> <span class="n" style="color: #333;">cat</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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261
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261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rate_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">site_rate</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getRate</span><span class="p">(</span><span class="n" style="color: #333;">cat</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">prop_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">site_rate</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getProp</span><span class="p">(</span><span class="n" style="color: #333;">cat</span><span class="p">);</span></span>
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262
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<td class="diff-line-num new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getModelFactory</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">site_rate</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getGammaShape</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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263
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="n" style="color: #333;">rate_val</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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264
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265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">rate_sqr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rate_val</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rate_val</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">coeff1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rate_val</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">prop_val</span><span class="p">;</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">coeff2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rate_val</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">coeff1</span><span class="p">;</span></span>
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266
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getModelFactory</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">computeTransDerv</span><span class="p">(</span><span class="n" style="color: #333;">value</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">rate_val</span><span class="p">,</span> <span class="n" style="color: #333;">trans_mat</span><span class="p">,</span> <span class="n" style="color: #333;">trans_derv1</span><span class="p">,</span> <span class="n" style="color: #333;">trans_derv2</span><span class="p">);</span></span>
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267
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269
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<pre style="margin: 0;"> <span id="LC269" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">trans_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_trans</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">trans_mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_derv1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">trans_derv1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">rate_val</span></span><span class="p">;</span></span>
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270
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<pre style="margin: 0;">-<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_derv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">trans_derv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">rate_sqr</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_trans</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">trans_mat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">prop_val</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_derv1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">trans_derv1</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">coeff1</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_derv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">trans_derv2</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;"><span class="idiff left right">coeff2</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// 2019-07-03: incorporate p_invar</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">p_invar</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">site_rate</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getPInvar</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">p_invar</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">num_states</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">sum_trans</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">num_states</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">p_invar</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">trans_size</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pair_freq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">Params</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getInstance</span><span class="p">().</span><span class="n" style="color: #333;">min_branch_length</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">sum_trans</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// lh -= pair_freq[i] * log(sum_trans[i]);</span></span>
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<li id="1d1fdc052f5fcf9ab26c74024f124949c4236777">
<a href="https://salsa.debian.org/med-team/iqtree/compare/2c73dfd20694ecad26fd3de621af6dfaf34d3ae5...f24fc79b601ae043ff5247d5ce3cd7f18e00824b#1d1fdc052f5fcf9ab26c74024f124949c4236777"><strong>alignment/superalignment.cpp</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">@@ -664,7 +664,7 @@ Alignment *SuperAlignment::removeIdenticalSeq(string not_remove, bool keep_two,</td>
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664
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">checked</span><span class="p">[</span><span class="n" style="color: #333;">seq1</span><span class="p">])</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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665
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<pre style="margin: 0;"> <span id="LC665" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">first_ident_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC666" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq1</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="n" style="color: #333;">seq2</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">getNSeq</span><span class="p">();</span> <span class="n" style="color: #333;">seq2</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC667" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getSeqName</span><span class="p">(</span><span class="n" style="color: #333;">seq2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">not_remove</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getSeqName</span><span class="p">(</span><span class="n" style="color: #333;">seq2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">not_remove</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">removed</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">seq2</span></span><span class="p"><span class="idiff right">]</span>)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC668" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">equal_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC669" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">part</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC670" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check if seq1 and seq2 are identical over all partitions</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">iqtree (1.6.12+dfsg-1) unstable; urgency=medium</span>
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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"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Wed, 04 Dec 2019 13:52:57 +0100</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">iqtree (1.6.11+dfsg-1) unstable; urgency=medium</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"> * New upstream version</span>
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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">@@ -13,7 +13,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> help2man,</span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> time,</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> chrpath</span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/iqtree</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/iqtree.git</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Homepage: http://www.cibiv.at/software/iqtree/</span>
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<a href="https://salsa.debian.org/med-team/iqtree/compare/2c73dfd20694ecad26fd3de621af6dfaf34d3ae5...f24fc79b601ae043ff5247d5ce3cd7f18e00824b#a7ac8f866fa5767febd882507b49374354178d30"><strong>main/phyloanalysis.cpp</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">@@ -3464,10 +3464,14 @@ void assignBootstrapSupport(const char *input_trees, int burnin, int max_count,</td>
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<pre style="margin: 0;"> <span id="LC3464" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">target_tree</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rooted</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">output_tree</span><span class="p">,</span></span>
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3465
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3465
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<pre style="margin: 0;"> <span id="LC3465" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out_prefix</span><span class="p">,</span> <span class="n" style="color: #333;">MExtTree</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mytree</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">tree_weight_file</span><span class="p">,</span></span>
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3466
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3466
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<pre style="margin: 0;"> <span id="LC3466" class="line" lang="cpp"> <span class="n" style="color: #333;">Params</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">params</span><span class="p">)</span> <span class="p">{</span></span>
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3467
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<pre style="margin: 0;">-<span id="LC3467" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//bool rooted = false</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC3467" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">bool</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">myrooted</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">rooted</span></span><span class="p">;</span></span>
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3468
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3468
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<pre style="margin: 0;"> <span id="LC3468" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// read the tree file</span></span>
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3469
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3469
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<pre style="margin: 0;"> <span id="LC3469" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Reading tree "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">target_tree</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ..."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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3470
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<pre style="margin: 0;">-<span id="LC3470" class="line" lang="cpp"> <span class="n" style="color: #333;">mytree</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">target_tree</span><span class="p">,</span> <span class="n" style="color: #333;">rooted</span><span class="p">);</span></span>
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3470
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<pre style="margin: 0;">+<span id="LC3470" class="line" lang="cpp"> <span class="n" style="color: #333;">mytree</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">target_tree</span><span class="p">,</span> <span class="n" style="color: #333;">myrooted</span><span class="p">);</span></span>
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3471
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<pre style="margin: 0;">+<span id="LC3471" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mytree</span><span class="p">.</span><span class="n" style="color: #333;">rooted</span><span class="p">)</span></span>
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3472
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<pre style="margin: 0;">+<span id="LC3472" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"rooted tree detected"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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3473
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<pre style="margin: 0;">+<span id="LC3473" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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3474
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<pre style="margin: 0;">+<span id="LC3474" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"unrooted tree detected"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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3471
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3475
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<pre style="margin: 0;"> <span id="LC3475" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// reindex the taxa in the tree to aphabetical names</span></span>
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3476
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<pre style="margin: 0;"> <span id="LC3476" class="line" lang="cpp"> <span class="n" style="color: #333;">NodeVector</span> <span class="n" style="color: #333;">taxa</span><span class="p">;</span></span>
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3477
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<pre style="margin: 0;"> <span id="LC3477" class="line" lang="cpp"> <span class="n" style="color: #333;">mytree</span><span class="p">.</span><span class="n" style="color: #333;">getTaxa</span><span class="p">(</span><span class="n" style="color: #333;">taxa</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="3512" 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="3516" 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">@@ -3512,8 +3516,11 @@ void assignBootstrapSupport(const char *input_trees, int burnin, int max_count,</td>
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3512
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3516
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<pre style="margin: 0;"> <span id="LC3516" class="line" lang="cpp"> <span class="p">}</span></span>
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3513
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3517
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<pre style="margin: 0;"> <span id="LC3517" class="line" lang="cpp"> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">sg</span><span class="p">.</span><span class="n" style="color: #333;">maxWeight</span><span class="p">();</span></span>
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3514
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<td class="diff-line-num new_line" data-linenumber="3518" 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">
3518
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<pre style="margin: 0;"> <span id="LC3518" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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3515
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<td class="diff-line-num new_line old" data-linenumber="3519" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3515" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_trees</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">input_trees</span><span class="p">,</span> <span class="n" style="color: #333;">rooted</span><span class="p">,</span> <span class="n" style="color: #333;">burnin</span><span class="p">,</span> <span class="n" style="color: #333;">max_count</span><span class="p">,</span></span>
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3519
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<pre style="margin: 0;">+<span id="LC3519" class="line" lang="cpp"> <span class="n" style="color: #333;">myrooted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rooted</span><span class="p">;</span></span>
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3520
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<pre style="margin: 0;">+<span id="LC3520" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_trees</span><span class="p">.</span><span class="n" style="color: #333;">init</span><span class="p">(</span><span class="n" style="color: #333;">input_trees</span><span class="p">,</span> <span class="n" style="color: #333;">myrooted</span><span class="p">,</span> <span class="n" style="color: #333;">burnin</span><span class="p">,</span> <span class="n" style="color: #333;">max_count</span><span class="p">,</span></span>
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3516
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3521
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<pre style="margin: 0;"> <span id="LC3521" class="line" lang="cpp"> <span class="n" style="color: #333;">tree_weight_file</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="3522" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
3522
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<pre style="margin: 0;">+<span id="LC3522" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mytree</span><span class="p">.</span><span class="n" style="color: #333;">rooted</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">boot_trees</span><span class="p">.</span><span class="n" style="color: #333;">isRooted</span><span class="p">())</span></span>
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3523
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<pre style="margin: 0;">+<span id="LC3523" class="line" lang="cpp"> <span class="n" style="color: #333;">outError</span><span class="p">(</span><span class="s" style="color: #d14;">"Target tree and tree set have different rooting"</span><span class="p">);</span></span>
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3517
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3524
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<pre style="margin: 0;"> <span id="LC3524" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_trees</span><span class="p">.</span><span class="n" style="color: #333;">convertSplits</span><span class="p">(</span><span class="n" style="color: #333;">taxname</span><span class="p">,</span> <span class="n" style="color: #333;">sg</span><span class="p">,</span> <span class="n" style="color: #333;">hash_ss</span><span class="p">,</span> <span class="n" style="color: #333;">SW_COUNT</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">params</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">support_tag</span><span class="p">);</span></span>
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3518
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3525
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<pre style="margin: 0;"> <span id="LC3525" class="line" lang="cpp"> <span class="n" style="color: #333;">scale</span> <span class="o" style="font-weight: 600;">/=</span> <span class="n" style="color: #333;">boot_trees</span><span class="p">.</span><span class="n" style="color: #333;">sumTreeWeights</span><span class="p">();</span></span>
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3519
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3526
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<pre style="margin: 0;"> <span id="LC3526" class="line" lang="cpp"> <span class="p">}</span></span>
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<li id="182d27852fc1f61eed93e31783224a351bfaea3c">
<a href="https://salsa.debian.org/med-team/iqtree/compare/2c73dfd20694ecad26fd3de621af6dfaf34d3ae5...f24fc79b601ae043ff5247d5ce3cd7f18e00824b#182d27852fc1f61eed93e31783224a351bfaea3c"><strong>main/phylotesting.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1405" 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="1405" 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">@@ -1405,7 +1405,7 @@ string testOneModel(string &model_name, Params ¶ms, Alignment *in_aln,</td>
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1405
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1405
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<pre style="margin: 0;"> <span id="LC1405" class="line" lang="cpp"> <span class="n" style="color: #333;">IQTree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">iqtree</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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1406
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1406
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<pre style="margin: 0;"> <span id="LC1406" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">in_aln</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isSuperAlignment</span><span class="p">())</span> <span class="p">{</span></span>
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1407
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1407
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<pre style="margin: 0;"> <span id="LC1407" class="line" lang="cpp"> <span class="n" style="color: #333;">SuperAlignment</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">saln</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">SuperAlignment</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">in_aln</span><span class="p">;</span></span>
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1408
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<pre style="margin: 0;">-<span id="LC1408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">brle</span>n_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">BRLEN_OPTIMIZE</span><span class="p">)</span></span>
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1408
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<pre style="margin: 0;">+<span id="LC1408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">params</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">partitio</span>n_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">BRLEN_OPTIMIZE</span><span class="p">)</span></span>
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1409
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1409
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<pre style="margin: 0;"> <span id="LC1409" class="line" lang="cpp"> <span class="n" style="color: #333;">iqtree</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PhyloSuperTree</span><span class="p">(</span><span class="n" style="color: #333;">saln</span><span class="p">);</span></span>
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1410
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<pre style="margin: 0;"> <span id="LC1410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span></span>
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<pre style="margin: 0;"> <span id="LC1411" class="line" lang="cpp"> <span class="n" style="color: #333;">iqtree</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">PhyloSuperTreePlen</span><span class="p">(</span><span class="n" style="color: #333;">saln</span><span class="p">,</span> <span class="n" style="color: #333;">brlen_type</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/iqtree/compare/2c73dfd20694ecad26fd3de621af6dfaf34d3ae5...f24fc79b601ae043ff5247d5ce3cd7f18e00824b#f239d8758cbcf834f3f5227bb6a482150c6d1695"><strong>tree/mtree.cpp</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">@@ -684,7 +684,7 @@ void MTree::readTree(istream &in, bool &is_rooted)</td>
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<pre style="margin: 0;"> <span id="LC684" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">branch_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">)</span> <span class="n" style="color: #333;">branch_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span><span class="p">;</span></span>
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685
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<pre style="margin: 0;"> <span id="LC685" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">branch_len</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span><span class="p">)</span></span>
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686
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<pre style="margin: 0;"> <span id="LC686" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">ERR_NEG_BRANCH</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">is_rooted</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">rooted</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">is_rooted</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC688" class="line" lang="cpp"> <span class="n" style="color: #333;">root</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newNode</span><span class="p">(</span><span class="n" style="color: #333;">leafNum</span><span class="p">,</span> <span class="n" style="color: #333;">ROOT_NAME</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cpp"> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addNeighbor</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="n" style="color: #333;">branch_len</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC690" class="line" lang="cpp"> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">addNeighbor</span><span class="p">(</span><span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">branch_len</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/iqtree/compare/2c73dfd20694ecad26fd3de621af6dfaf34d3ae5...f24fc79b601ae043ff5247d5ce3cd7f18e00824b#eb644fdc89c64d146a52d5305e863af83a4f64ab"><strong>tree/mtreeset.cpp</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">@@ -235,7 +235,7 @@ void MTreeSet::checkConsistency() {</td>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> </span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="n" style="color: #333;">iterator</span> <span class="n" style="color: #333;">it</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC238" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rooted</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">f<span class="idiff left right">alse</span></span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">rooted</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f<span class="idiff left">ront</span></span><span class="p"><span class="idiff">()</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff right">rooted</span></span><span class="p">;</span></span>
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">it</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">end</span><span class="p">();</span> <span class="n" style="color: #333;">it</span><span class="o" style="font-weight: 600;">++</span><span class="p">,</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span></span>
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