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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/seaview">Debian Med / seaview</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/seaview/commit/bd91f32fc06a9080ae0e6bbb88c7643a4cdc963d">bd91f32f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-09T14:09:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 4.7</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seaview/commit/1d3e947cf1bcfbbe1e3af9ccda817069394a2a6c">1d3e947c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-09T14:09:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/4.7'
Update to upstream version '4.7'
with Debian dir 7bfbf77f2950957665e42f90ad024c3a1bd05b24</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seaview/commit/a2bbaa7c782a74226153b2b41f20024828134d36">a2bbaa7c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-09T14:09:47+02:00</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/seaview/commit/3b90e3912ae65cea51d2a9ef62b1f8654379880a">3b90e391</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-09T14:16:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Patch applied upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/seaview/commit/b5aefb54f7e92027ac1e0776d4e13dea591aa77b">b5aefb54</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-05-09T14:20:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Drop patch since upstream has fixed Makefile; Re-add example which was lost by accident
</pre>
</li>
</ul>
<h4>13 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
</a>
</li>
<li class="file-stats">
<a href="#69e27356ef629022720d868ab0c0e3394775b6c1">
<span class="new-file">
+
README
</span>
</a>
</li>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#0ac61ff92e2295bb773688ae78fb76813319eafc">
<span class="deleted-file">
−
debian/patches/re-add_missing_ldlibs.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="deleted-file">
−
debian/patches/series
</span>
</a>
</li>
<li class="file-stats">
<a href="#c12b5341097e6583d50eac28bd9c7c937500766c">
debian/seaview.examples
</a>
</li>
<li class="file-stats">
<a href="#45cc856bb01edcdbf63fe3f71fe0a88efa118590">
<span class="new-file">
+
example.nxs
</span>
</a>
</li>
<li class="file-stats">
<a href="#52273abf25871d8fe4213e1c91f4ad2bf44aa78c">
<span class="new-file">
+
seaview.appdata.xml
</span>
</a>
</li>
<li class="file-stats">
<a href="#8e243f34391f295535f892f8860929f4088e3e78">
seaview.html
</a>
</li>
<li class="file-stats">
<a href="#060189d181394c992152d6af27da0946d67695ea">
<span class="new-file">
+
tbe.cxx
</span>
</a>
</li>
<li class="file-stats">
<a href="#2be9eda7c11e18a541fd58e783a923efa38e8ff3">
<span class="new-file">
+
tbe.h
</span>
</a>
</li>
<li class="file-stats">
<a href="#e9736b31785e6496d884a05c1ff46bf5b83ad99f">
treedraw.h
</a>
</li>
<li class="file-stats">
<a href="#3bb2c0d8693fbdda425f55aff63ef52cf340505a">
trees.cxx
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,7 +21,7 @@</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"><span class="nv" style="color: teal;">CONFIG</span> <span class="o" style="font-weight: 600;">?=</span> fltk-config</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="22" 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="22" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nv" style="color: teal;">PDF_PS_FLAGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: navy;">-DNO_PDF</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="23" 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="23" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"></span>
</pre>
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<td class="diff-line-num new_line old" data-linenumber="24" 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="LC24" class="line" lang="make"><span class="nv" style="color: teal;">EXTRALIBS</span> <span class="o" style="font-weight: 600;">=</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$(CONFIG)</span> <span class="nt" style="color: navy;">--use-images</span> <span class="nt" style="color: navy;">--ldflags</span><span class="sb" style="color: #d14;">`</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"><span class="nv" style="color: teal;">EXTRALIBS</span> <span class="o" style="font-weight: 600;">=</span> <span class="sb" style="color: #d14;">`</span><span class="nv" style="color: teal;">$(CONFIG)</span> <span class="nt" style="color: navy;">--use-images</span> <span class="nt" style="color: navy;">--ldflags</span><span class="sb" style="color: #d14;">`</span><span class="idiff left"> </span><span class="nt" style="color: navy;"><span class="idiff">-ldl</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff">-lpthread</span></span><span class="idiff"> </span><span class="nt" style="color: navy;"><span class="idiff right">-lz</span></span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="26" 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="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"><span class="nv" style="color: teal;">CC</span> <span class="o" style="font-weight: 600;">=</span> gcc</span>
</pre>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"><span class="nv" style="color: teal;">CXX</span> <span class="o" style="font-weight: 600;">=</span> g++</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" 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="38" 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">@@ -38,7 +38,7 @@ OBJECTS = seaview.o custom.o use_mase_files.o regions.o load_seq.o align.o xfmat</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC38" class="line" lang="make">comlines.o resource.o nexus.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make">viewasprots.o racnuc_fetch.o concatenate.o statistics.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make">trees.o treedraw.o addbootstrap.o least_squares_brl.o <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="make">pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o Fl_Native_File_Chooser_FLTK.o</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make">pseudoterminal.o unrooted.o pdf_or_ps.o svg.o threads.o <span class="idiff left right">tbe.o </span>Fl_Native_File_Chooser_FLTK.o</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"> </span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"><span class="nv" style="color: teal;">COBJECTS</span> <span class="o" style="font-weight: 600;">=</span> raa_acnuc.o parser.o md5.o zsockr.o misc_acnuc.o dnapars.o protpars.o seq.o phylip.o lwl.o bionj.o phyml_util.o</span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"></span>
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<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#69e27356ef629022720d868ab0c0e3394775b6c1"><strong>README</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"> HOW TO COMPILE SEAVIEW ON UNIX/LINUX SYSTEMS</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">The seaview program requires the FLTK library for its graphical user interface.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Version 1.3.0 or later of FLTK is necessary.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">The FLTK library is available as packages for a number of Linux distributions.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">If this package is installed on your system, go to step II.</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">If no such package is available for your system, or if version 1.3.0 is not available,</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">or if you don't want to use such package, you can compile the FLTK library as follows.</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">I COMPILING THE FLTK LIBRARY FROM SOURCE</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"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">The source code of the FLTK library is available at the "Download" item of http://www.fltk.org/.</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">- Get the stable release source archive, currently fltk-1.3.2-source.tar.gz</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">- Compile the FLTK library on your system:</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> cd fltk-1.3.2</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> ./configure</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> make</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">It's not necessary to do "make install".</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">II COMPILING THE SEAVIEW PROGRAM</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">================================</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">First unpack the seaview source archive (seaview.tar.gz).</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">IIa Preparing the seaview makefile</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">If the FLTK library is installed on your system (i.e., include files in /usr/include/FL,</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">and libraries at /usr/lib/libfltk*), go to step IIb.</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Otherwise, edit Makefile from the seaview source directory which contains these 5 lines:</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">FLTK = /usr/include</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">#uncomment the next 3 lines to use custom installed FLTK library</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">#FLTK = $(HOME)/fltk-1.3.2</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">#IFLTK = -I$(FLTK)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">#LFLTK = -L$(FLTK)/lib</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">Transform these lines into:</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">#FLTK = /usr/include</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">#uncomment the next 3 lines to use custom installed FLTK library</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">FLTK = $(HOME)/fltk-1.3.2</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">IFLTK = -I$(FLTK)</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">LFLTK = -L$(FLTK)/lib</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">and also change the FLTK = $(HOME)/fltk-1.3.2 line so it gives the location in your system</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">of the top of the FLTK source tree.</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">IIb Compile/link the seaview program</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">In the seaview source directory, run</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">make</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">III Install seaview external programs</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">=====================================</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Seaview drives 4 external programs (clustalo, muscle, Gblocks, phyml). Linux executables</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">of these are available from the linux items of http://pbil.univ-lyon1.fr/software/seaview.html</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">They are also available as packages of most Linux distributions.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">These programs should be put in your PATH or in the same directory as the seaview</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">executable for seaview to drive them.</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">By default seaview searches for the phyml executable under the names PhyML-3.1_linux32</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">or PhyML-3.1_linux64. If they are installed under other names on your system, seaview </span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">will ask you for their name and location which are remembered for subsequent runs.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"></span></pre>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">seaview (1:4.7-1) UNRELEASED; 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"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Drop patch since upstream has fixed Makefile</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Re-add example which was lost by accident</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"> -- Andreas Tille <tille@debian.org> Wed, 09 May 2018 14:09:47 +0200</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">seaview (1:4.6.5-1) 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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<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#0ac61ff92e2295bb773688ae78fb76813319eafc"><strong>debian/patches/re-add_missing_ldlibs.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">Description: Add ldflags used in Makefile of last version to build successfully</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Last-Update: Fri, 27 Apr 2018 17:20:34 +0200</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/Makefile</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -21,7 +21,7 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> CONFIG ?= fltk-config</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> PDF_PS_FLAGS ?= -DNO_PDF</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-EXTRALIBS = `$(CONFIG) --use-images --ldflags`</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+EXTRALIBS = `$(CONFIG) --use-images --ldflags` -ldl -lpthread -lz</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> CC = gcc</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> CXX = g++</span></pre>
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<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">re-add_missing_ldlibs.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#c12b5341097e6583d50eac28bd9c7c937500766c"><strong>debian/seaview.examples</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">debian/example_files/*</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right"># </span>example.nxs</span></pre>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">example.nxs</span></pre>
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<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#45cc856bb01edcdbf63fe3f71fe0a88efa118590"><strong>example.nxs</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#NEXUS</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">[saved by seaview on Thu Mar 19 11:25:58 2015]</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">BEGIN DATA;</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> DIMENSIONS NTAX=54 NCHAR=456;</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> FORMAT DATATYPE=DNA</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> GAP=-</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> ;</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">MATRIX</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">[1] D82069.PE1</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">---------atgaagcctgaggaaatttcaagaggaaaagcttttggactgctgaaagcc</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">caacaggaagagaggttggatgggatcaacaagcacttcctcgatgatcccaagtacagc</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">agtgatgaggatctgcagtccaaactggaggccttcaagacgaagtacatggagtttgat</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">ctgaatggcaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">gttcccaagacccatctagagctgaagaaattaattagagaggtgtccagtggc---tcc</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">gaggagacgttcagttactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacaccag---aagccaactggt</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">cccccagccaagaaagctatttctgagttgccctaa</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">[2] 'AB019540.AIF-1'</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">------------atggacagcacagctcaaggaggtaaagcatttggtcttctcaagtct</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">caccaggaagaaaaattgaactctatcaatgaggcttttctctcagatccccaatatgca</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">gaagaggaagacctcagctcaaagcttgaagcatttaaaaagaaatacatggagtttgat</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">cttaacgacaaaggagaaatagatattatgggtttgaaacggatgctggaaaaactcgga</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">ttggccaagactcacttggagctgaaaaagatgatgtcagaggtctgtggaggaacatcg</span>
</pre>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">aaagaaactttcggctaccacgacttcctgaatatgatgctgggaaaaagaaatgcaatt</span>
</pre>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">ctaaaactgatcttgatgtttgaaggcatgggaaaggagcacgagtccaaagatgcggca</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">ccacctcctcgcaaaaccttttcagacctgccctga</span>
</pre>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">[3] AB000818.PE1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="28" 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">
28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">------atgagccagagcaaggatttgcagggaggaaaagcttttggactgctgaaagcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="29" 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">
29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">cagcaggaagagaggttggatgggatcaacaagcacttcctcgatgatcccaagtacagc</span>
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<td class="diff-line-num new new_line" data-linenumber="30" 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">
30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">agtgatgaggatctgcagtccaaactggaggccttcaagacgaagtacatggagtttgat</span>
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<td class="diff-line-num new new_line" data-linenumber="31" 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">
31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">ctgaatggcaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
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<td class="diff-line-num new new_line" data-linenumber="32" 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">
32
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">gttcccaagacccatctagagctgaagaaattaattagagaggtgtccagtggc---tcc</span>
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<td class="diff-line-num new new_line" data-linenumber="33" 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">
33
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">gaggagacgttcagttactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="34" 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">
34
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacaccag---aagccaactggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="35" 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">
35
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">cccccagccaagaaagctatttctgagttgccctaa</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="36" 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">
36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">[4] AB012309.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="37" 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">
37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">------atgccttccaaccagaatttacaaggcgggaaagccttcgggttactcaaagca</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="38" 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">
38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">cagcagagggagaagctggatgaaatcaataaggagtttatggaagatcagaagtaccgg</span>
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<td class="diff-line-num new new_line" data-linenumber="39" 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">
39
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">gatgaagaggatttgcaagagaagctagattcttttaaaaataaatatgctgagtttgac</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="40" 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">
40
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">ctgaacgatcagggggatatcgacatgatgggcttgaagcgaatgatggagaagttgggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="41" 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">
41
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">gtgccaaagactcacctggagatgaagaaaatgatctcagaggtgacaggaggt---tgc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="42" 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">
42
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">agcgacaccatcaactacagggactttgtgaaaatgatgcttggcaagcgatcagctgtt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="43" 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">
43
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">ctcaaactggttatgatgtttgaagacaaagctaatgaggccagcggtaaacccgatgga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="44" 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">
44
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">cccccacccaagcgtgacatcaccacccttccataa</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="45" 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">
45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">[5] 'AB013745.AIF-1'</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="46" 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">
46
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="47" 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">
47
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="48" 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">
48
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="49" 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">
49
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="50" 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">
50
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="51" 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">
51
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="52" 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">
52
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="53" 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">
53
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
</pre>
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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="plaintext">[6] AB035322</span>
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<td class="diff-line-num new new_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">
55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">atgtcggtcgcactcagcaacaggttccaaggagggaaggcgttcggtttgctcaaagcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="56" 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">
56
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">cggcaggagaagaggctcgaggagatcaatcgggagttcctctgtgaccagaagtacagt</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="57" 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">
57
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">gatgaagagaacctgccggaaaagctcgcagccttcaaagagaaatacatggagtttgac</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="58" 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">
58
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">ctgaataatgaaggcgagattgatctgatgtctttaaagaggatgatggagaagctgggg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="59" 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">
59
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcggaggtgacagggggt---gtc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="60" 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">
60
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">agtgacaccatctcctaccgagactttgtgaatatgatgctgggcaagcggtcggctgtc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="61" 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">
61
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">ctcaagctggtcatgatgtttgaaggaaaagccaacgagagcagcccgaagccagctggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="62" 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">
62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">ccacctccagagcgagacatcgccagcctgccttga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">[7] AB036423.IBA1</span>
</pre>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">---------atgaagcctgaggagatttcaagaggaaaagcttttggactgctgaaggcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="65" 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">
65
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="66" 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">
66
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="67" 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">
67
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="68" 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">
68
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="69" 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">
69
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="70" 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">
70
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="71" 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">
71
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="72" 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">
72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">[8] AB036423.PE2</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="73" 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">
73
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="74" 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">
74
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="75" 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">
75
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="76" 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">
76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="77" 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">
77
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="78" 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">
78
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="79" 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">
79
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="80" 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">
80
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="81" 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">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">[9] AB094629.IBA2</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="82" 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">
82
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">atgtcggtcgcactcagcaacaggttccaaggagggaaggcgttcggtttgctcaaagcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="83" 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">
83
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">cggcaggagaagaggctcgaggagatcaatcgggagttcctctgtgaccagaagtacagt</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="84" 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">
84
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">gatgaagagaacctgccggaaaagctcgcagccttcaaagagaaatacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="85" 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">
85
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">ctgaataatgaaggcgagattgatctgatgtctttaaagaggatgatggagaagctgggg</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="86" 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">
86
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcggaggtgacagggggt---gtc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="87" 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">
87
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">agtgacaccatctcctaccgagactttgtgaatatgatgctgggcaagcggtcggctgtc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="88" 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">
88
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">ctcaagctggtcatgatgtttgaaggaaaagccaacgagagcagcccgaagccagctggc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="89" 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">
89
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">ccacctccagagcgagacatcgccagcctgccttga</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="90" 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">
90
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">[10] AB128049.AIF1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="91" 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">
91
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="92" 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">
92
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaatttctagatgatcccaaatacagc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="93" 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">
93
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">agtgatgaggatctgctctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="94" 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">
94
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">cttaatggaaacggcgatattgatatcatgtccctgaagcgaatgctggagaaacttggg</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="95" 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">
95
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="96" 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">
96
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="97" 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">
97
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="98" 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">
98
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">cccccagccaagaaagctatttctgagttgccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="99" 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">
99
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">[11] AF074959.PE1</span>
</pre>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
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<td class="diff-line-num new new_line" data-linenumber="105" 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">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
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<td class="diff-line-num new new_line" data-linenumber="106" 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">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="108" 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">
108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">[12] AF109719.PE7</span>
</pre>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
</pre>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="113" 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">
113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="114" 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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="116" 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">
116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">[13] AF129756.PE18</span>
</pre>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcagactgctgaaggcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="121" 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">
121
</td>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
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<td class="diff-line-num new new_line" data-linenumber="125" 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">
125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">[14] AF348450.PE1</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">------atgagcgaaactagggatttacagggaggaaaagcctttgggctgcggaaagcc</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">cagcaggaagagagaatcaatgaaatcaaccagcaattcctggatgatcccaaatacagc</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">agtgatgaggacctgccctccaaactggaagccttcaagaagaaatacatggagtttgac</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">ctgaatgaagatggaggtatcgatatcatgtccctgaagcgaatgatggagaaacttggg</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">gttcccaagacccacctggagctaaagaaattaatcatggaggtatccagtggc---cct</span>
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<td class="diff-line-num new new_line" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">ggggagactttcagctactctgactttctcaagatgatgttgggcaagagatctgccatt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="133" 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">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaagagaaagcaagagaacaggag---aagccaacaggt</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">ctcccagccaagaaagctatctctgagttgccctga</span>
</pre>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">[15] AJ506968.AIF1</span>
</pre>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">------------atggagaaaaatgttcaaggaggcaaagcgtatggacttctcaaaagt</span>
</pre>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">caccaggaagagaaactgaactcgatcaatgaggcttttcagtcagatcctcaatatgcc</span>
</pre>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">gaagaggaggaccttggctccaaacttgaaatgtttaaaaataaatacatggagtttgat</span>
</pre>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">ctcaatgatcaaggagacatagacataatggggttaaaacggatgcttgaaaaacttgga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">gtggccaagactcacctagaactgaaaaagatgatgtcagaggtgattggtggggcctcg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">aaagacacaatcagctaccacgacttcctaaatatgatgctggggaaaagaaatgcaatt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">ctcaaactgatcctgatgtttgaaggaatggggaaggagcaggagtcaaaagtcgttggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">ccacctggtcgcaaaaccttttcagacctgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="144" 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">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">[16] AK006184.PE1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="148" 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">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
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<td class="diff-line-num new new_line" data-linenumber="150" 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">
150
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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">
151
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
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<td class="diff-line-num new new_line" data-linenumber="152" 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">
152
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="153" 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">
153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">[17] AK006562.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="154" 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">
154
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="155" 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">
155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="156" 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">
156
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="157" 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">
157
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="160" 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">
160
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="161" 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">
161
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="162" 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">
162
</td>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">[18] AK022845.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="163" 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">
163
</td>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">atgtcgggcgagctcagcaacaggttccaaggagggaaggcgttcggcttgctcaaagcc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="164" 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">
164
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">cggcaggagaggaggctggccgagatcaaccgggagcttctgtgtgaccagaagtacagt</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">gatgaagagaaccttccagaaaagctcacagccttcaaagagaagtacatggagtttgac</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="166" 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">
166
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">ctgaacaatgaaggcgagattgacctgatgtctttaaagaggatgatggagaagcttggt</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="167" 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">
167
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcagaggtgacaggaggg---gtc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="168" 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">
168
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">agtgacactatatcctaccgagactttgtgaacatgatgctggggaaacggtcggctgtc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="169" 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">
169
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">ctcaagttagtcatgatgtttgaaggaaaagccaacgagagcagccccaagccagttggc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="170" 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">
170
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">ccccctccagagagagacattgctagcctgccctga</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">[19] AK028955.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">atgtcggtcgcactcagcaacaggttccaaggagggaaggcgttcggtttgctcaaagcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">cggcaggagaagaggctcgaggagatcaatcgggagttcctctgtgaccagaagtacagt</span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">gatgaagagaacctgccggaaaagctcgcagccttcaaagagaaatacatggagtttgac</span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">ctgaataatgaaggcgagattgatctgatgtctttaaagaggatgatggagaagctgggg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcggaggtgacagggggt---gtc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">agtgacaccatctcctaccgagactttgtgaataagatgctgggcaagcggtcggctgtc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">ctcaagctggtcatgatgtttgaaggaaaagccaacgagagcagcccgaagccagctggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
179
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">ccacctccagagcgagacatcgccagcctgccttga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="180" 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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">[20] AK045539.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="181" 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">
181
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">atgtcggtcgcactcagcaacaggttccaaggagggaaggcgttcggtttgctcaaagcc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="182" 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">
182
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">cggcaggagaagaggctcgaggagatcaatcgggagttcctctgtgaccagaagtacagt</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">gatgaagagaacctgccggaaaagctcgcagccttcaaagagaaatacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">ctgaataatgaaggcgagattgatctgatgtctttaaagaggatgatggagaagctgggg</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcggaggtgacagggggt---gtc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="186" 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">
186
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">agtgacaccatctcctaccgagactttgtgaatatgatgctgggcaagcggtcggctgtc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="187" 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">
187
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">ctcaagctggtcatgatgtttgaaggaaaagccaacgagagcagcccgaagccagctggc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">ccacctccagagcgagacatcgccagcctgccttga</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="189" 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">[21] AK091912.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="190" 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">
190
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">atgtcgggcgagctcagcaacaggttccaaggagggaaggcgttcggcttgctcaaagcc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="191" 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">
191
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">cggcaggagaggaggctggccgagatcaaccgggagtttctgtgtgaccagaagtacagt</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="192" 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">
192
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">gatgaagagaaccttccagaaaagctcacagccttcaaagagaagtacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="193" 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">
193
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">ctg------------------------atgtctttaaagaggatgatggagaagcttggt</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="194" 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">
194
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcagaggtgacaggaggg---gtc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="195" 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">
195
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">agtgacactatatcctaccgagactttgtgaacatgatgctggggaaacggtcggctgtc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">ctcaagttagtcatgatgtttgaaggaaaagccaacgagagcagccccaagccagttggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">ccccctccagagagagacattgctagcctgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">[22] AL136566.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">atgtcgggcgagctcagcaacaggttccaaggagggaaggcgttcggcttgctcaaagcc</span>
</pre>
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200
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">cggcaggagaggaggctggccgagatcaaccgggagtttctgtgtgaccagaagtacagt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">gatgaagagaaccttccagaaaagctcacagccttcaaagagaagtacatggagtttgac</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="202" 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">
202
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">ctgaacaatgaaggcgagattgacctgatgtctttaaagaggatgatggagaagcttggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="203" 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">
203
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcagaggtgacaggaggg---gtc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="204" 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">
204
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">agtgacactatatcctaccgagactttgtgaacatgatgctggggaaacggtcggctgtc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="205" 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">
205
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">ctcaagttagtcatgatgtttgaaggaaaagccaacgagagcagccccaagccagttggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="206" 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">
206
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">ccccctccagagagagacattgctagcctgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="207" 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">
207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">[23] AL157938.PE2</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="208" 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">
208
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">atgtcgggcgagctcagcaacaggttccaaggagggaaggcgttcggcttgctcaaagcc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="209" 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">
209
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">cggcaggagaggaggctggccgagatcaaccgggagtttctgtgtgaccagaagtacagt</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="210" 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">
210
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">gatgaagagaaccttccagaaaagctcacagccttcaaagagaagtacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="211" 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">
211
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">ctgaacaatgaaggcgagattgacctgatgtctttaaagaggatgatggagaagcttggt</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="212" 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">
212
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcagaggtgacaggaggg---gtc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="213" 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">
213
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">agtgacactatatcctaccgagactttgtgaacatgatgctggggaaacggtcggctgtc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="214" 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">
214
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">ctcaagttagtcatgatgtttgaaggaaaagccaacgagagcagccccaagccagttggc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="215" 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">
215
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">ccccctccagagagagacattgctagcctgccctga</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="216" 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">
216
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">[24] AL157938.PE3</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="217" 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">
217
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">atgtcgggcgagctcagcaacaggttccaaggagggaaggcgttcggcttgctcaaagcc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="218" 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">
218
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">cggcaggagaggaggctggccgagatcaaccgggagtttctgtgtgaccagaagtacagt</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="219" 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">
219
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">gatgaagagaaccttccagaaaagctcacagccttcaaagagaagtacatggagtttgac</span>
</pre>
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</tr>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">ctg------------------------atgtctttaaagaggatgatggagaagcttggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="221" 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">
221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcagaggtgacaggaggg---gtc</span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">agtgacactatatcctaccgagactttgtgaacatgatgctggggaaacggtcggctgtc</span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">ctcaagttagtcatgatgtttgaaggaaaagccaacgagagcagccccaagccagttggc</span>
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224
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">ccccctccagagagagacattgctagcctgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="225" 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">
225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">[25] AL662801.PE45</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="227" 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">
227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="228" 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">
228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="229" 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">
229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="230" 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">
230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
</pre>
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231
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="232" 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">
232
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="233" 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">
233
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="234" 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">
234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">[26] AL662847.AIF1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="235" 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">
235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="236" 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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="237" 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">
237
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="238" 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">
238
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="239" 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">
239
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="240" 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">
240
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="241" 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">
241
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="242" 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">
242
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="243" 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">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">[27] AL805934.AIF1</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="244" 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">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
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<td class="diff-line-num new new_line" data-linenumber="245" 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">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
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<td class="diff-line-num new new_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
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<td class="diff-line-num new new_line" data-linenumber="248" 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">
248
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
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<td class="diff-line-num new new_line" data-linenumber="249" 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">
249
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="250" 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">
250
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="251" 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">
251
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">[28] AL833896.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="253" 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">
253
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">atgtcgggcgagctcagcaacaggttccaaggagggaaggcgttcggcttgctcaaagcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="254" 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">
254
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">cggcaggagaggaggctggccgagatcaaccgggagtttctgtgtgaccagaagtacagt</span>
</pre>
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255
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">gatgaagagaaccttccagaaaagctcacagccttcaaagagaagtacatggagtttgac</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="256" 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">
256
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">ctgaacaatgaaggcgagattgacctgatgtctttaaagaggatgatggagaagcttggt</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcagaggtgacaggaggg---gtc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="258" 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">
258
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">agtgacactatatcctaccgagactttgtgaacatgatgctggggaaacggtcggctgtc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">ctcaagttagtcatgatgtttgaaggaaaagccaacgagagcagccccaagccagttggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="260" 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">
260
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">ccccctccagagagagacattgctagcctgccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="261" 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">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">[29] AL928893.PE3</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="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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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">atgtcggtcgcactcagcaacaggttccaaggagggaaggcgttcggtttgctcaaagcc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="263" 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">
263
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">cggcaggagaagaggctcgaggagatcaatcgggagttcctctgtgaccagaagtacagt</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="264" 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">
264
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">gatgaagagaacctgccggaaaagctcgcagccttcaaagagaaatacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="265" 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">
265
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">ctgaataatgaaggcgagattgatctgatgtctttaaagaggatgatggagaagctgggg</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="266" 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">
266
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcggaggtgacagggggt---gtc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="267" 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">
267
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">agtgacaccatctcctaccgagactttgtgaatatgatgctgggcaagcggtcggctgtc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">ctcaagctggtcatgatgtttgaaggaaaagccaacgagagcagcccgaagccagctggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="269" 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">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">ccacctccagagcgagacatcgccagcctgccttga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">[30] AY359067.PE1</span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">atgtcgggcgagctcagcaacaggttccaaggagggaaggcgttcggcttgctcaaagcc</span>
</pre>
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272
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">cggcaggagaggaggctggccgagatcaaccgggagtttctgtgtgaccagaagtacagt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="273" 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">
273
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">gatgaagagaaccttccagaaaagctcacagccttcaaagagaagtacatggagtttgac</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="274" 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">
274
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">ctgaacaatgaaggcgagattgacctgatgtctttaaagaggatgatggagaagcttggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="275" 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">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcagaggtgacaggaggg---gtc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="276" 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">
276
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">agtgacactatatcctaccgagactttgtgaacatgatgctggggaaacggtcggctgtc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="277" 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">
277
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">ctcaagttagtcatgatgtttgaaggaaaagccaacgagagcagccccaagccagttggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">ccccctccagagagagacattgctagcctgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">[31] BA000025.AIF1</span>
</pre>
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280
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_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">
281
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="282" 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">
282
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="283" 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">
283
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="285" 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">
285
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="286" 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">
286
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="287" 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">
287
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="288" 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">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">[32] BC009474.AIF1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="289" 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">
289
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="290" 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">
290
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="291" 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">
291
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="292" 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">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="293" 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">
293
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="294" 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">
294
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="295" 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">
295
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="296" 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">
296
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">[33] BC021539.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="298" 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">
298
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="299" 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">
299
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="300" 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">
300
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaaatacatggagtttgat</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="301" 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">
301
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="302" 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">
302
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="303" 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">
303
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="304" 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">
304
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="305" 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">
305
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="306" 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">
306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">[34] BC024599.PE1</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="307" 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">
307
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">atgtcggtcgcactcagcaacaggttccaaggagggaaggcgttcggtttgctcaaagcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="308" 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">
308
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">cggcaggagaagaggctcgaggagatcaatcgggagttcctctgtgaccagaagtacagt</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="309" 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">
309
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">gatgaagagaacctgccggaaaagctcgcagccttcaaagagaaatacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="310" 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">
310
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">ctgaataatgaaggcgagattgatctgatgtctttaaagaggatgatggagaagctgggg</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="311" 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">
311
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcggaggtgacagggggt---gtc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="312" 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">
312
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">agtgacaccatctcctaccgagactttgtgaatatgatgctgggcaagcggtcggctgtc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="313" 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">
313
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">ctcaagctggtcatgatgtttgaaggaaaagccaacgagagcagcccgaagccagctggc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="314" 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">
314
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">ccacctccagagcgagacatcgccagcctgccttga</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<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">
315
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">[35] BC073304.MGC8069</span>
</pre>
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<td class="diff-line-num new new_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">
316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">------atgtcttctaataacattaaacaaggtggcaaagctttcgtgatccaaaaggca</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">cagcaggagcacagactagaggaggtgaacaaggagttccttaaagatgaaaaatacaag</span>
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<td class="diff-line-num new new_line" data-linenumber="318" 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">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">gatgatgaggacttggataaaaaactgatgtcctttaaaaaaaagtacatggaatttgac</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">cttaaccaacaaggagagctggatatgatgggcctcaagaaaatgttggagaatctggga</span>
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320
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">gccgctaagacccatttagaagttaagaaattgatatatgaagtgacaggaggc---aaa</span>
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<td class="diff-line-num new new_line" data-linenumber="321" 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">
321
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">agtgaggcaatcagctatcaggattttgtaaccatgatgcttggaaaacgttcagccata</span>
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<td class="diff-line-num new new_line" data-linenumber="322" 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">
322
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">atgaaatttatcatgatgtttgagggaaaaaatgaagtcacaagtcccaagcccatgggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="323" 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">
323
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">ccaccaccaaagagagacatcagcagcctaccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="324" 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">
324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">[36] BC074259.MGC8401</span>
</pre>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">------atgtcttccaataacattaaacaaggtggcaaagctttcgtgatccaaaaggcg</span>
</pre>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">cagcaggagcacagactggaggaggtgaacaaggagttccttaaagatgaaaaatacaag</span>
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327
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">gatgacgaggacttggataaaaaactgatgtcctttaaaaaaaagtacatggaatttgac</span>
</pre>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">cttaaccaccaaggagagctggatatgatgggcctgaagaaaatgatggagaacctggga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="329" 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">
329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">gctgctaaaacccatttagaagttaagaaactgatatatgaagtgacgggaggc---aaa</span>
</pre>
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330
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">agtgaggcaatcagctaccgggattttgtaaccatgatgctgggaaaacgttctgccgtg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="331" 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">
331
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">atgaaatttatcatgatgtttgagggaaaaaatgaagtcacatgtcccaagccaaagggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="332" 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">
332
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext">ccaccacccaagagagacatcagcagccttccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="333" 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">
333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">[37] BC084814.MGC8401</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="334" 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">
334
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">------atgtcttccaataacattaaacaaggtggcaaagctttcgtgatccaaaaggcg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="335" 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">
335
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">cagcaggagcacagactggaggaggtgaacaaggagttccttaaagatgaaaaatacaag</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="336" 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">
336
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">gatgacgaggacttggataaaaaactgatgtcctttaaaaaaaagtacatggaatttgac</span>
</pre>
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337
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">cttaaccaccaaggagagctggatatgatgggcctgaagaaaatgatggagaacctggga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="338" 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">
338
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">gctgctaaaacccatttagaagttaagaaactgatatatgaagtgacgggaggc---aaa</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="339" 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">
339
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">agtgaggcaatcagctaccgggattttgtaaccatgatgctgggaaaacgttctgccgtg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="340" 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">
340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext">atgaaatttatcatgatgtttgagggaaaaaatgaagtcacatgtcccaagccaaagggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="341" 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">
341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">ccaccacccaagagagacatcagcagccttccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="342" 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">
342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">[38] BC102890.AIF1</span>
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<td class="diff-line-num new new_line" data-linenumber="343" 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">
343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">------atgagcgaaactagggatttacagggaggaaaagcctttgggctgcggaaagcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="344" 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">
344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext">cagcaggaagagagaatcaatgaaatcaaccagcaattcctggatgatcccaaatacagc</span>
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<td class="diff-line-num new new_line" data-linenumber="345" 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">
345
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">agtgatgaggacctgccctccaaactggaagccttcaagaagaaatacatggagtttgac</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="346" 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">
346
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">ctgaatgaagatggaggtatcgatatcatgtccctgaagcgaatgatggagaaacttggg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="347" 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">
347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">gttcccaagacccacctggagctaaagaaattaatcatggaggtatccagtggc---cct</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="348" 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">
348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext">ggggagactttcagctactctgactttctcaagatgatgttgggcaagagatctgccatt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="349" 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">
349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaagagaaagcaagagaacaggag---aagccaacaggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="350" 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">
350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">ctcccagccaagaaagctatctctgagttgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="351" 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">
351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext">[39] BC126840.C9ORF58</span>
</pre>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext">atgtcggtcgcgttcagcaacaggttccaaggagggaaagccttcggtttgctcaaagcc</span>
</pre>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">cggcaggagaggaggctggccgagatcaaccgggagttcctctgcgaccaaaagtacagt</span>
</pre>
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354
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">gatgaagagaacctgccggaaaagctcacagcctttaaagagaagtacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="355" 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">
355
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">ctgaacaatgagggagagattgatctgatgtctttgaagaggatgatggagaagcttggg</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="356" 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">
356
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcggaggtgacaggtggg---gtc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="357" 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">
357
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">agcgacaccatctcctaccgagacttcgtgaacatgatgctggggaagcggtcggcggtc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="358" 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">
358
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">cttaagctagtcatgatgtttgaaggaaaagccaacgaaggcagctccaagccagtcggg</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="359" 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">
359
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">ccccctccagagagagacatcgccagcctgccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="360" 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">
360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext">[40] BX248305.PE3</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="361" 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">
361
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="362" 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">
362
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="363" 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">
363
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="364" 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">
364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="365" 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">
365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
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<td class="diff-line-num new new_line" data-linenumber="366" 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">
366
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
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<td class="diff-line-num new new_line" data-linenumber="367" 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">
367
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
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<td class="diff-line-num new new_line" data-linenumber="368" 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">
368
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="369" 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">
369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext">[41] BX571730.PE3</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="370" 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">
370
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext">------atgccttccaacatggacttacaaggcggaaaagccttcgggttgctcaaagct</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="371" 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">
371
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">cagcagagggacaagctggaggaaatcaataaggagttcatggaagatcagaagtacaga</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="372" 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">
372
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext">gacgaagaggacttgcctgaaaagctggattcttttaaaaataaatatgcagagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="373" 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">
373
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext">ctgaacgatcaaggggaaatcgacatgatgggcttgaagcgaatgatggagaagttgggt</span>
</pre>
</td>
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<td class="diff-line-num new new_line" data-linenumber="374" 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">
374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext">gtgccaaaaactcatctgcagatgaagaaaatgatctctgaggtgacaggaggc---tgc</span>
</pre>
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</tr>
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375
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext">agtgacaccatcaactacagggattttgtgaaaatgatgctcggcaagcgatcagctgtt</span>
</pre>
</td>
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376
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext">ctcaaactggttatgatgtttgaagacaaagctaatgggtccagctgtaagcctgatggg</span>
</pre>
</td>
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<td class="diff-line-num new new_line" data-linenumber="377" 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">
377
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext">cctccacccaaacgtgacatcaccagcctaccatag</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="378" 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">
378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext">[42] BX883046.AIF1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="379" 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">
379
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">------atgagccagagcaaggatttgcagggaggaaaagcttttggactgctgaaagcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="380" 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">
380
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext">caacaggaagagaggttggatgggatcaacaagcacttcctcgatgatcccaagtacagc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="381" 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">
381
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">agtgatgaggatctgcagtccaaactggaggccttcaagacgaagtacatggagtttgat</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext">ctgaatggcaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="383" 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">
383
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext">gttcccaagacccatctagagctgaagaaattaattagagaggtgtccagtggc---tcc</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="384" 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">
384
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext">gaggagacgttcagttactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="385" 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">
385
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacaccag---aagccaactggt</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="386" 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">
386
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext">cccccagccaagaaagctatttctgagttgccctaa</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="387" 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">
387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">[43] CR762385.PE3</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="plaintext">------atgccttccaacatggacttacaaggcggaaaagccttcgggttgctcaaagct</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="389" 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">
389
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC389" class="line" lang="plaintext">cagcagagggacaagctggaggaaatcaataaggagttcatggaagatcagaagtacaga</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="390" 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">
390
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC390" class="line" lang="plaintext">gacgaagaggacttgcctgaaaagctggattcttttaaaaataaatatgcagagtttgac</span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="391" 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">
391
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC391" class="line" lang="plaintext">ctgaacgatcaaggggaaatcgacatgatgggcttgaagcgaatgatggagaagttgggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
392
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext">gtgccaaaaactcatctgcagatgaagaaaatgatctctgaggtgacaggaggc---tgc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="393" 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">
393
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC393" class="line" lang="plaintext">agtgacaccatcaactacagggattttgtgaaaatgatgctcggcaagcgatcagctgtt</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="394" 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">
394
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC394" class="line" lang="plaintext">ctcaaactggttatgatgtttgaagacaaagctaatgggtccagctgtaagcctgatggg</span>
</pre>
</td>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="395" 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">
395
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC395" class="line" lang="plaintext">cctccacccaaacgtgacatcaccagcctaccatag</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="396" 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">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="plaintext">[44] CR857925.PE1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="397" 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">
397
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC397" class="line" lang="plaintext">atgtcgggcgagctcagcaacaggttccaaggagggaaggcgttcggcttgctcaaagcc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="398" 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">
398
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC398" class="line" lang="plaintext">cggcaggagaggaggctggccgagatcgaccgggagtttctctgtgaccagaagtacagt</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="399" 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">
399
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC399" class="line" lang="plaintext">gatgaagagaaccttccagaaaagctcacagccttcaaagagaagtacatggagtttgac</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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="400" 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">
400
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC400" class="line" lang="plaintext">ctgaacaatgaaggcgagattgacctaatgtctttaaagaggatgatggagaagcttggt</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="401" 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">
401
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC401" class="line" lang="plaintext">gtccccaagacccacctggagatgaagaagatgatctcagaggtgacaggaggg---gtc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="402" 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">
402
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC402" class="line" lang="plaintext">agtgacaccatatcctaccgagactttgtgaacatgatgctggggaaacggtcggctgtc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="403" 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">
403
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC403" class="line" lang="plaintext">ctcaagctagtcatgatgtttgaaggaaaggccaacgagagcagccccaagccagttggc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="404" 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">
404
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC404" class="line" lang="plaintext">ccccctccagagagagacattgctagcctgccctga</span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="405" 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">
405
</td>
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="plaintext">[45] CT010265</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="406" 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">
406
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC406" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="407" 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">
407
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC407" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="408" 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">
408
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC408" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="409" 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">
409
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC409" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="410" 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">
410
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC410" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
</pre>
</td>
</tr>
<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="0" 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">
</td>
<td class="diff-line-num new new_line" data-linenumber="411" 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">
411
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC411" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
</td>
</tr>
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<td class="diff-line-num new new_line" data-linenumber="412" 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">
412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
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<td class="diff-line-num new new_line" data-linenumber="413" 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">
413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctag</span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="plaintext">[46] CT010385</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
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417
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC417" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaaatacatggagtttgat</span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="419" 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">
419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="421" 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">
421
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC421" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="422" 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">
422
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC422" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctag</span>
</pre>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="plaintext">[47] D86382.IBA1</span>
</pre>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
</pre>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
</pre>
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426
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC426" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
</pre>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="428" 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">
428
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC428" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="429" 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">
429
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC429" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="430" 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">
430
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC430" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="431" 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">
431
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC431" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="432" 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">
432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="plaintext">[48] D86438.IBA1</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="433" 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">
433
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC433" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="434" 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">
434
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC434" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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="435" 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">
435
</td>
<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC435" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
</pre>
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436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
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438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
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439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
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440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="plaintext">[49] EF070983.PE1</span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
</pre>
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443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
</pre>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
</pre>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
</pre>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
</pre>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
</pre>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
</pre>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="plaintext">[50] U17919.PE1</span>
</pre>
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451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="plaintext">------atgagccagagcaaggatttgcagggaggaaaagcttttggactgctgaaagcc</span>
</pre>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="plaintext">cagcaggaagagaggttggatgggatcaacaagcacttcctcgatgatcccaagtacagc</span>
</pre>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="plaintext">agtgatgaggatctgcagtccaaactggaggccttcaagacgaagtacatggagtttgat</span>
</pre>
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454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="plaintext">ctgaatggcaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="plaintext">gttcccaagacccatctagagctgaagaaattaattagagaggtgtccagtggc---tcc</span>
</pre>
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456
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC456" class="line" lang="plaintext">gaggagacgttcagttactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacaccag---aagccaactggt</span>
</pre>
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458
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC458" class="line" lang="plaintext">cccccagccaagaaagctatttctgagttgccctaa</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="459" 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">
459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="plaintext">[51] U19713.PE1</span>
</pre>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="plaintext">[52] 'U49392.AIF-1'</span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctacacgatcccaaatatagc</span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccttgaaacgaatgctggagaaacttgga</span>
</pre>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
</pre>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
</pre>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaggaaa---accaacacgccc</span>
</pre>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext">cccagccaagaaagccctatctga------------</span>
</pre>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="plaintext">[53] U82792.PE1</span>
</pre>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="plaintext">------atgagccaaagcagggatttgcagggaggaaaagcttttggactgctgaaggcc</span>
</pre>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="plaintext">cagcaggaagagaggctggaggggatcaacaagcaattcctcgatgatcccaaatacagc</span>
</pre>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="plaintext">aatgatgaggatctgccgtccaaacttgaagccttcaaggtgaagtacatggagtttgat</span>
</pre>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="plaintext">ctgaatggaaatggagatatcgatattatgtccttgaagcgaatgctggagaaacttggg</span>
</pre>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="plaintext">gttcccaagacccacctagagctgaagagattaattagagaggtgtccagtggc---tcc</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="483" 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">
483
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC483" class="line" lang="plaintext">gaggagacgttcagctactctgactttctcagaatgatgctgggcaagagatctgccatc</span>
</pre>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="plaintext">ttgagaatgattctgatgtatgaggagaaaaacaaagaacacaag---aggccaactggt</span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="plaintext">cccccagccaagaaagctatctccgagctgccctga</span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="plaintext">[54] Y14768.PE3</span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="plaintext">------atgagccaaaccagggatttacagggaggaaaagctttcggactgctgaaggcc</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="plaintext">cagcaggaagagaggctggatgagatcaacaagcaattcctagacgatcccaaatatagc</span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="plaintext">agtgatgaggatctgccctccaaactggaaggcttcaaagagaaatacatggagtttgac</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext">cttaatggaaatggcgatattgatatcatgtccctgaaacgaatgctggagaaacttgga</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext">gtccccaagactcacctagagctaaagaaattaattggagaggtgtccagtggc---tcc</span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="plaintext">ggggagacgttcagctaccctgactttctcaggatgatgctgggcaagagatctgccatc</span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext">ctaaaaatgatcctgatgtatgaggaaaaagcgagagaaaaggaa---aagccaacaggc</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext">cccccagccaagaaagctatctctgagttgccctga</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext">;</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext">END;</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext">BEGIN NOTES;</span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext"> TEXT TAXON=1 TEXT='D82069.PE1 CDS /codon_start=1 /product="iba1, ionized calcium binding adapter mo</span>
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499
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext"> TEXT TAXON=2 TEXT='AB019540.AIF-1 CDS /codon_start=1 /transl_table=1 /gene="AIF-1" /product="allogr</span>
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501
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"> TEXT TAXON=3 TEXT='AB000818.PE1 CDS /codon_start=1 /transl_table=1 /product="MRF-1" /db_xref="GOA:P</span>
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503
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"> TEXT TAXON=4 TEXT='AB012309.PE1 CDS /codon_start=1 /transl_table=1 /product="allograft inflammatory</span>
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505
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext"> TEXT TAXON=5 TEXT='AB013745.AIF-1 CDS /codon_start=1 /transl_table=1 /gene="AIF-1" /product="allogr</span>
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507
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext"> TEXT TAXON=6 TEXT='AB035322 Mus musculus mRNA for ionized calcium binding adapter molecule 2 (Iba2)</span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext"> TEXT TAXON=7 TEXT='AB036423.IBA1 CDS /codon_start=1 /transl_table=1 /gene="iba1" /product="ionized </span>
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="plaintext"> TEXT TAXON=8 TEXT='AB036423.PE2 CDS /codon_start=1 /transl_table=1 /gene="iba1" /product="ionized c</span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="plaintext"> TEXT TAXON=9 TEXT='AB094629.IBA2 CDS /codon_start=1 /transl_table=1 /gene="iba2" /product="ionized </span>
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="plaintext"> TEXT TAXON=10 TEXT='AB128049.AIF1 CDS /codon_start=1 /transl_table=1 /gene="AIF1" /product="allograf</span>
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext"> TEXT TAXON=11 TEXT='AF074959.PE1 CDS /codon_start=1 /product="allograft inflammatory factor-1" /note</span>
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext"> TEXT TAXON=12 TEXT='AF109719.PE7 CDS /codon_start=1 /product="AIF-1" /note="allograft inflammatory f</span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext"> TEXT TAXON=13 TEXT='AF129756.PE18 CDS /codon_start=1 /product="AIF-1" /note="anti-inflammatory facto</span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext"> TEXT TAXON=14 TEXT='AF348450.PE1 CDS /codon_start=1 /product="allograft inflammatory factor-1" /note</span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext"> TEXT TAXON=15 TEXT='AJ506968.AIF1 CDS /gene="aif1" /product="allograft inflammatory factor 1" /db_xr</span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext"> TEXT TAXON=16 TEXT='AK006184.PE1 CDS /codon_start=1 /transl_table=1 /note="ALLOGRAFT INFLAMMATORY FA</span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext"> TEXT TAXON=17 TEXT='AK006562.PE1 CDS /codon_start=1 /transl_table=1 /note="ALLOGRAFT INFLAMMATORY FA</span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext"> TEXT TAXON=18 TEXT='AK022845.PE1 CDS /codon_start=1 /db_xref="GOA:Q9BQI0" /db_xref="HGNC:28904" /db_</span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext"> TEXT TAXON=19 TEXT='AK028955.PE1 CDS /codon_start=1 /transl_table=1 /note="IONIZED CALCIUM BINDING A</span>
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="plaintext"> TEXT TAXON=31 TEXT='BA000025.AIF1 CDS /codon_start=1 /transl_table=1 /gene="AIF1" /product="Allograf</span>
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="plaintext"> TEXT TAXON=32 TEXT='BC009474.AIF1 CDS /codon_start=1 /gene="AIF1" /product="allograft inflammatory f</span>
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="plaintext"> TEXT TAXON=33 TEXT='BC021539.PE1 CDS /codon_start=1 /product="Aif1 protein" /db_xref="GOA:O70200"</span>
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="plaintext"> TEXT TAXON=34 TEXT='BC024599.PE1 CDS /codon_start=1 /gene="2810003C17Rik" /product="RIKEN cDNA 28100</span>
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="plaintext"> TEXT TAXON=36 TEXT='BC074259.MGC8401 CDS /codon_start=1 /gene="MGC84014" /product="MGC84014 protein"</span>
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="plaintext"> TEXT TAXON=38 TEXT='BC102890.AIF1 CDS /codon_start=1 /gene="AIF1" /product="allograft inflammatory f</span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="plaintext"> TEXT TAXON=39 TEXT='BC126840.C9ORF58 CDS /codon_start=1 /gene="C9orf58" /product="ionized calcium bi</span>
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575
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="plaintext"> TEXT TAXON=40 TEXT='BX248305.PE3 CDS /gene="AIF1" /locus_tag="DASS-82G15.2-001" /standard_name="OTTH</span>
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577
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="plaintext"> TEXT TAXON=41 TEXT='BX571730.PE3 CDS /gene="DKEY-35I22.4" /locus_tag="DKEY-35I22.4-001" /standard_na</span>
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579
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="plaintext"> TEXT TAXON=42 TEXT='BX883046.AIF1 CDS /codon_start=1 /gene="Aif1" /product="allograft inflammatory f</span>
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581
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="plaintext"> TEXT TAXON=43 TEXT='CR762385.PE3 CDS /gene="DKEY-35I22.4" /locus_tag="DKEY-35I22.4-001" /standard_na</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="plaintext"> TEXT TAXON=44 TEXT='CR857925.PE1 CDS /codon_start=1 /gene="DKFZp469A1629" /product="hypothetical pro</span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="plaintext"> TEXT TAXON=45 TEXT='CT010265 Mus musculus full open reading frame cDNA clone RZPDo836F0551D for gene</span>
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="plaintext"> TEXT TAXON=46 TEXT='CT010385 Mus musculus full open reading frame cDNA clone RZPDo836E0453D for gene</span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="plaintext"> TEXT TAXON=47 TEXT='D86382.IBA1 CDS /transl_table=1 /gene="iba1" /product="Iba1 (ionized calcium bin</span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="plaintext"> TEXT TAXON=48 TEXT='D86438.IBA1 CDS /codon_start=1 /transl_table=1 /gene="iba1" /product="Iba1 (ioni</span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="plaintext"> TEXT TAXON=49 TEXT='EF070983.PE1 CDS /codon_start=1 /product="allograft inflammatory factor 1 isofor</span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="plaintext"> TEXT TAXON=50 TEXT='U17919.PE1 CDS /codon_start=1 /product="allograft inflammatory factor-1" /note="</span>
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597
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="plaintext"> TEXT TAXON=51 TEXT='U19713.PE1 CDS /codon_start=1 /product="allograft-inflammatory factor-1" /db_xre</span>
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599
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="plaintext"> TEXT TAXON=52 TEXT='U49392.AIF-1 CDS /codon_start=1 /gene="AIF-1" /product="allograft inflammatory f</span>
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601
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="plaintext"> TEXT TAXON=53 TEXT='U82792.PE1 CDS /codon_start=1 /product="allograft inflammatory factor-1" /note="</span>
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603
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="plaintext"> TEXT TAXON=54 TEXT='Y14768.PE3 CDS /gene="AIF1" /product="allograft inflamatory factor-1" /note="U19</span>
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605
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606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="plaintext">END;</span>
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="plaintext">BEGIN SETS;</span>
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="plaintext"> TAXSET 'good seqs' = 1-14;</span>
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="plaintext"> TAXSET 'good seqs2' = 1 4 7 15 29 35 38 44 52;</span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="plaintext">END;</span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="plaintext">BEGIN TREES;</span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="plaintext"> TREE 'BioNJ_tree'= [BioNJ 402 sites J-C]((((((((U19713.PE1:-0.00000,(EF070983.PE1:-0.00000,</span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="plaintext">(D86438.IBA1:-0.00000,(BX248305.PE3:-0.00000,(BC009474.AIF1:-0.00000,(BA000025.AIF1:-0.00000,</span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="plaintext">(AL805934.AIF1:-0.00001,(AL662847.AIF1:-0.00001,(AL662801.PE45:-0.00002,</span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="plaintext">AB094629.IBA2:-0.00042):0.00021):0.00011):0.00006):0.02880):0.10555,((CR762385.PE3:0.00000,</span>
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631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="plaintext">BX571730.PE3:0.00000):0.05262,AB012309.PE1:0.03992):0.12386):0.03135,(BC073304.MGC8069:0.03323,</span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="plaintext">(BC084814.MGC8401:0.00000,BC074259.MGC8401:0.00000):0.01825):0.21336):0.03264)</span>
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633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="plaintext">;</span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="plaintext"> TREE 'PhyML_tree'= [PhyML ln(L)=-2269.6 456 sites GTR](((((((AF074959.PE1:0.00000,AF109719.PE7:0.00000)</span>
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635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="plaintext">:0.00000,(AB036423.PE2:0.00000,AB013745.AIF-1:0.00000):0.00000):0.00000,</span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="plaintext">AB036423.IBA1:0.03730):0.01864,(AB000818.PE1:0.00000,D82069.PE1:0.03507)</span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="plaintext">:0.03518):0.06236,AB128049.AIF1:0.04232):0.14213,(AB012309.PE1:0.18990,</span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="plaintext">(AB094629.IBA2:0.00000,AB035322:0.00000):0.13348):0.13688):0.03873,AB019540.AIF-1:0.28594)</span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="plaintext">;</span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="plaintext"> TREE 'Dnapars_tree'= [Dnapars, 4 best trees (100% consensus), 653 steps, 402 sites (246 informative)</span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="plaintext">](((((((D82069.PE1:0.03234,AB000818.PE1:0.00000):0.00000,BX883046.AIF1:0.00249)</span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="plaintext">:0.00000,U17919.PE1:0.00000):0.02778,((((((((((AB013745.AIF-1:0.00000,AB036423.PE2:0.00000)</span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="plaintext">:0.00000,AF074959.PE1:0.00000):0.00000,AF109719.PE7:0.00000):0.00000,AK006184.PE1:0.00000)</span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="plaintext">:0.00000,AK006562.PE1:0.00000):0.00000,(BC021539.PE1:0.00000,CT010385:0.00000)</span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="plaintext">:0.00249):0.00000,CT010265:0.00000):0.00000,D86382.IBA1:0.00000):0.00000,</span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="plaintext">U82792.PE1:0.00000):0.00560,AB036423.IBA1:0.02923):0.01907):0.04490,((AB128049.AIF1:0.00746,</span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="plaintext">(((((((((((AF129756.PE18:0.00249,AL662801.PE45:0.00000):0.00000,AL662847.AIF1:0.00000)</span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="plaintext">:0.00000,AL805934.AIF1:0.00000):0.00000,BA000025.AIF1:0.00000):0.00000,</span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="plaintext">BC009474.AIF1:0.00000):0.00000,BX248305.PE3:0.00000):0.00000,D86438.IBA1:0.00000)</span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="plaintext">:0.00000,EF070983.PE1:0.00000):0.00000,U19713.PE1:0.00000):0.00000,U49392.AIF-1:0.06219)</span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="plaintext">:0.00000,Y14768.PE3:0.00000):0.01244):0.03664,(AF348450.PE1:0.00000,BC102890.AIF1:0.00000)</span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="plaintext">:0.06598):0.02990):0.10853,(AB019540.AIF-1:0.09301,AJ506968.AIF1:0.07118)</span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="plaintext">:0.00249):0.02765):0.04465):0.10866):0.04076);</span>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="plaintext">BEGIN seaview;</span>
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<pre style="margin: 0;">+<span id="LC748" class="line" lang="plaintext"> TEXT HEADER TEXT=' saved by seaview on Tue Feb 19 15:24:41 2013</span>
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<pre style="margin: 0;">+<span id="LC749" class="line" lang="plaintext"> saved by seaview on Mon Feb 11 17:21:33 2013</span>
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<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#52273abf25871d8fe4213e1c91f4ad2bf44aa78c"><strong>seaview.appdata.xml</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="xml"><span class="cp" style="color: #999; font-weight: 600;"><?xml version="1.0" encoding="UTF-8"?></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="xml"><span class="c" style="color: #998; font-style: italic;"><!-- Copyright 2015 Manolo Gouy <manolo.gouy_at_univ-lyon1.fr> --></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="xml"><span class="nt" style="color: navy;"><component</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"desktop"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="xml"> <span class="nt" style="color: navy;"><id></span>seaview.desktop<span class="nt" style="color: navy;"></id></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="xml"> <span class="nt" style="color: navy;"><metadata_license></span>CC0-1.0<span class="nt" style="color: navy;"></metadata_license></span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="xml"> <span class="nt" style="color: navy;"><project_license></span>GPL-3.0<span class="nt" style="color: navy;"></project_license></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="xml"> <span class="nt" style="color: navy;"><name></span>SeaView<span class="nt" style="color: navy;"></name></span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="xml"> <span class="nt" style="color: navy;"><summary></span>GUI for multiple sequence alignment and molecular phylogeny<span class="nt" style="color: navy;"></summary></span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="xml"> <span class="nt" style="color: navy;"><description></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="xml"><span class="nt" style="color: navy;"><p></span>SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny.<span class="nt" style="color: navy;"></p></span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="xml"><span class="nt" style="color: navy;"><ul></span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="xml"> <span class="nt" style="color: navy;"><li></span>SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP,</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="xml"> MASE, Newick) of DNA and protein sequences and of phylogenetic trees.<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="xml"> <span class="nt" style="color: navy;"><li></span>SeaView drives programs muscle or Clustal-Omega for multiple sequence alignment, </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="xml"> and also allows to use any external alignment algorithm able to read and write FASTA-formatted files.<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="xml"> <span class="nt" style="color: navy;"><li></span>Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites.<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="xml"> <span class="nt" style="color: navy;"><li></span>SeaView computes phylogenetic trees by:<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="xml"> <span class="nt" style="color: navy;"><li></span>- parsimony, using PHYLIP's dnapars/protpars algorithm,<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="xml"> <span class="nt" style="color: navy;"><li></span>- distance, with NJ or BioNJ algorithms on a variety of evolutionary distances,<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="xml"> <span class="nt" style="color: navy;"><li></span>- maximum likelihood, driving program PhyML 3.1.<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="xml"> <span class="nt" style="color: navy;"><li></span>SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files.<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="xml"> <span class="nt" style="color: navy;"><li></span>SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet.<span class="nt" style="color: navy;"></li></span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="xml"><span class="nt" style="color: navy;"></ul></span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="xml"> <span class="nt" style="color: navy;"></description></span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="xml"> <span class="nt" style="color: navy;"><screenshots></span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="xml"> <span class="nt" style="color: navy;"><screenshot</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"default"</span><span class="nt" style="color: navy;">></span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="xml"> <span class="nt" style="color: navy;"><image></span>http://doua.prabi.fr/binaries/seaview4.png<span class="nt" style="color: navy;"></image></span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="xml"> <span class="nt" style="color: navy;"><caption></span>The main alignment window used in the color-by-codon mode<span class="nt" style="color: navy;"></caption></span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="xml"> <span class="nt" style="color: navy;"></screenshot></span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="xml"> <span class="nt" style="color: navy;"><screenshot></span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="xml"> <span class="nt" style="color: navy;"><image></span>http://doua.prabi.fr/binaries/seaview-tree.png<span class="nt" style="color: navy;"></image></span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="xml"> <span class="nt" style="color: navy;"><caption></span>The tree window with some zoom-in applied<span class="nt" style="color: navy;"></caption></span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="xml"> <span class="nt" style="color: navy;"></screenshot></span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="xml"> <span class="nt" style="color: navy;"><screenshot></span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="xml"> <span class="nt" style="color: navy;"><image></span> http://doua.prabi.fr/software/seaview_data/PhyML-dialog.png<span class="nt" style="color: navy;"></image></span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="xml"> <span class="nt" style="color: navy;"><caption></span>Dialog window to perform Maximum-Likelihood tree-building<span class="nt" style="color: navy;"></caption></span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="xml"> <span class="nt" style="color: navy;"></screenshot></span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="xml"> <span class="nt" style="color: navy;"></screenshots></span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="xml"> <span class="nt" style="color: navy;"><url</span> <span class="na" style="color: teal;">type=</span><span class="s" style="color: #d14;">"homepage"</span><span class="nt" style="color: navy;">></span>http://doua.prabi.fr/software/seaview<span class="nt" style="color: navy;"></url></span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="xml"> <span class="nt" style="color: navy;"><updatecontact></span>manolo.gouy_at_univ-lyon1.fr<span class="nt" style="color: navy;"></updatecontact></span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="xml"> <span class="nt" style="color: navy;"><developer_name></span>Manolo Gouy<span class="nt" style="color: navy;"></developer_name></span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="xml"> <span class="nt" style="color: navy;"><keywords></span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="xml"> <span class="nt" style="color: navy;"><keyword></span>molecular phylogeny<span class="nt" style="color: navy;"></keyword></span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="xml"> <span class="nt" style="color: navy;"><keyword></span>phylogenetic tree<span class="nt" style="color: navy;"></keyword></span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="xml"> <span class="nt" style="color: navy;"><keyword></span>sequence alignment<span class="nt" style="color: navy;"></keyword></span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="xml"> <span class="nt" style="color: navy;"><keyword></span>parsimony<span class="nt" style="color: navy;"></keyword></span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="xml"> <span class="nt" style="color: navy;"><keyword></span>neighbor-joining/keyword></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="xml"> <span class="nt" style="color: navy;"><keyword></span>maximum likelihood<span class="nt" style="color: navy;"></keyword></span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="xml"> <span class="nt" style="color: navy;"></keywords></span></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">@@ -44,7 +44,7 @@ Molecular Biology and Evolution 27(2):221-224.</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="html">SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny.<span class="nt" style="color: navy;"></a></span> </span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="html">Comput. Appl. Biosci., 12:543-548.</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="html"><span class="nt" style="color: navy;"><p></span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="html">Version 4.<span class="idiff left right">6.5</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="html">Version 4.<span class="idiff left right">7</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="html"></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Binaries and full source code available from <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">http://doua.prabi.fr/software/seaview</span><span class="nt" style="color: navy;">></span>http://doua.prabi.fr/software/seaview<span class="nt" style="color: navy;"></a></span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="html"></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">@@ -56,16 +56,17 @@ Version 4.6.5</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="html"><span class="nt" style="color: navy;"><p></span>Seaview drives the Muscle, Clustal Omega, Gblocks, and PhyML programs and uses code from the PHYLIP</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="html">package for parsimony. Please quote:</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="html"><span class="nt" style="color: navy;"><ul><li></span>Edgar R.C. (2004) <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">http://dx.doi.org/10.1093/nar/gkh340</span><span class="nt" style="color: navy;">></span>MUSCLE: multiple sequence alignment with high accuracy and </span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="html"> high throughput.<span class="nt" style="color: navy;"></a></span> <span class="idiff left right">Nucleic Acids Res.</span> 32(5):1792-1797.</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="html"> high throughput.<span class="nt" style="color: navy;"></a></span> <span class="nt" style="color: navy;"><span class="idiff left"><i></span></span><span class="idiff">Nucleic Acids Res.</span><span class="nt" style="color: navy;"><span class="idiff right"></i></span></span> 32(5):1792-1797.</span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>Sievers F. et al. (2011) <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">http://dx.doi.org/10.1038/msb.2011.75</span><span class="nt" style="color: navy;">></span>Fast, scalable generation of high-quality protein </span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="html">multiple sequence alignments using Clustal Omega.<span class="nt" style="color: navy;"></a></span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="html"> <span class="idiff left right">Molecular Systems Biology</span> 7:539.</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="html"> <span class="nt" style="color: navy;"><span class="idiff left"><i></span></span><span class="idiff">Molecular Systems Biology</span><span class="nt" style="color: navy;"><span class="idiff right"></i></span></span> 7:539.</span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>Castresana J. (2000) <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">http://mbe.oxfordjournals.org/content/17/4/540.full</span><span class="nt" style="color: navy;">></span>Selection of conserved blocks from multiple alignments for their </span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="html"> use in phylogenetic analysis.<span class="nt" style="color: navy;"></a></span> <span class="idiff left right">Molecular Biology and Evolution 17(4):540-552. </span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="html"> use in phylogenetic analysis.<span class="nt" style="color: navy;"></a></span> <span class="nt" style="color: navy;"><span class="idiff left"><i></span></span><span class="idiff">Molecular Biology and Evolution</span><span class="nt" style="color: navy;"><span class="idiff"></i></span></span><span class="idiff right"> 17(4):540-552.</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. (2010) </span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="html"> <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">http://dx.doi.org/10.1093/sysbio/syq010</span><span class="nt" style="color: navy;">></span>New Algorithms and Methods to Estimate Maximum-Likelihood </span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="html"> Phylogenies: Assessing the Performance of PhyML 3.0<span class="nt" style="color: navy;"></a></span>. <span class="idiff left right">Systematic Biology</span> 59(3):307-321.</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="html"> Phylogenies: Assessing the Performance of PhyML 3.0<span class="nt" style="color: navy;"></a></span>. <span class="nt" style="color: navy;"><span class="idiff left"><i></span></span><span class="idiff">Systematic Biology</span><span class="nt" style="color: navy;"><span class="idiff right"></i></span></span> 59(3):307-321.</span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>Felsenstein J. (2013) <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">http://evolution.genetics.washington.edu/phylip.html</span><span class="nt" style="color: navy;">></span>PHYLIP<span class="nt" style="color: navy;"></a></span> version 3.696.</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="html"><span class="nt" style="color: navy;"><li></span>Lemoine F., Domelevo Entfellner J.-B., Wilkinson E., Correia D., Dávila Felipe M., De Oliveira T. <span class="err" style="color: #a61717; background-color: #e3d2d2;">&</span> Gascuel O. (2018) <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">http://dx.doi.org/10.1038/s41586-018-0043-0</span><span class="nt" style="color: navy;">></span>Renewing Felsenstein’s phylogenetic bootstrap in the era of big data.<span class="nt" style="color: navy;"></a></span> <span class="nt" style="color: navy;"><i></span>Nature<span class="nt" style="color: navy;"></i></span> 556:452-456.</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="html">Seaview uses the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">http://www.fltk.org</span><span class="nt" style="color: navy;">></span>FLTK<span class="nt" style="color: navy;"></a></span> project for its user interface.</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">@@ -592,6 +593,7 @@ The weights of all equally parsimonious trees add up to 1 for each bootstrap rep</td>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="html"> <span class="nt" style="color: navy;"><br><u></span> ignore all gap sites:<span class="nt" style="color: navy;"></u></span> if on, all gap-containing sites are excluded from analysis;</span>
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<pre style="margin: 0;"> <span id="LC594" class="line" lang="html"> if off, not all sequence pairs use the same set of sites for computation of distances.</span>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="html"> <span class="nt" style="color: navy;"><br><u></span> Bootstrap:<span class="nt" style="color: navy;"></u></span> performs bootstrap evaluation of clade statistical support (can be interrupted).</span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="html"> Bootstrap supports can be optionally computed with the <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">https://doi.org/10.1038/s41586-018-0043-0</span><span class="nt" style="color: navy;">></span>Transfer Bootstrap Expectation<span class="nt" style="color: navy;"></a></span> method.</span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="html"> Furthermore, if "Show bootstrap trees" is checked,</span>
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="html"> individual bootstrap trees will appear in a second tree window, in addition to the main distance tree window.</span>
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="html"> <span class="nt" style="color: navy;"><br><u></span> User tree:<span class="nt" style="color: navy;"></u></span> computes least squares branch lengths for selected user tree topology.</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">@@ -606,8 +608,17 @@ Phylogenies: Assessing the Performance of PhyML 3.0</a>.</td>
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="html">Systematic Biology 59(3):307-321. </span>
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="html"> <span class="nt" style="color: navy;"><br><u></span> Model:<span class="nt" style="color: navy;"></u></span> select one among a variety of evolutionary models.</span>
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="html"> <span class="nt" style="color: navy;"><br><u></span> Branch support:<span class="nt" style="color: navy;"></u></span> can be omitted (None) or estimated either by the approximate likelihood </span>
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<pre style="margin: 0;">-<span id="LC609" class="line" lang="html"> ratio test approach (aLRT) or by bootstrap. In the last case, if "Show bootstrap trees" is checked,</span>
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<pre style="margin: 0;">-<span id="LC610" class="line" lang="html"> individual bootstrap trees will appear in a second tree window, in addition to the main PhyML tree window.</span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="html"> ratio test approach (aLRT) or by bootstrap. The bootstrap branch support can be computed by</span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="html"> two methods:</span>
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="html"> <span class="nt" style="color: navy;"><ul><li></span> The 'standard' method (Felsenstein's) counts the fraction of replicates containing each internal</span>
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="html"> branch of the reference tree.</span>
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="html"> <span class="nt" style="color: navy;"><li></span> The 'Transfer Bootstrap Expectation' method (TBE) proposed by Lemoine <span class="nt" style="color: navy;"><i></span>et al.<span class="nt" style="color: navy;"></i></span>:</span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="html"> <span class="nt" style="color: navy;"><a</span> <span class="na" style="color: teal;">href=</span><span class="s" style="color: #d14;">https://doi.org/10.1038/s41586-018-0043-0</span><span class="nt" style="color: navy;">></span>Renewing Felsenstein’s phylogenetic bootstrap in the era of big data<span class="nt" style="color: navy;"></a></span>.</span>
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="html"> <span class="nt" style="color: navy;"></ul></span></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="html"> If "Transfer Bootstrap Expectation method" is checked, both methods for computing</span>
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="html"> bootstrap supports are used and displayed in two tree windows.</span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="html"> With both bootstrap methods, if "Show bootstrap trees" is checked,</span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="html"> individual bootstrap trees will appear in yet another tree window.</span>
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<pre style="margin: 0;"> <span id="LC622" class="line" lang="html"> <span class="nt" style="color: navy;"><br><u></span> Nucleotide/Amino acid equilibrium frequencies:<span class="nt" style="color: navy;"></u></span> Residue frequencies can be estimated by counting</span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="html"> their frequencies in the sequence alignment ("Empirical" option). Alternatively, they can be optimized by </span>
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="html"> maximum likelihood ("Optimized" option for DNA data) or fixed to a set of model-given values ("Model-given"</span>
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<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#060189d181394c992152d6af27da0946d67695ea"><strong>tbe.cxx</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tbe.h"</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <assert.h></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</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;">preptree</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fd_nj_plot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"><span class="k" style="font-weight: 600;">extern</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;">ecrit_arbre_parenth_unrooted</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fd_nj_plot</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">root</span><span class="p">);</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><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;">TBE_Compute</span><span class="p">(</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;">reftree</span><span class="p">,</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;">boottrees</span><span class="p">){</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_branches</span><span class="p">;</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_branches</span><span class="p">;</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parsing reference tree</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fd_reftree</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span><span class="p">));</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"> <span class="n" style="color: #333;">fd_reftree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reftree</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"> <span class="n" style="color: #333;">fd_reftree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reftree</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC15" 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;">mess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">preptree</span><span class="p">(</span><span class="n" style="color: #333;">fd_reftree</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//TBE_PrintTree(fd_reftree);</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Parsing bootstrap trees</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fd_boot</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">calloc</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boottrees</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">current_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boottrees</span><span class="p">;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rank</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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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="n" style="color: #333;">ref_branches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TBE_Assign_Branch_Ids</span><span class="p">(</span><span class="n" style="color: #333;">fd_reftree</span><span class="p">);</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> </span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// For each bootstrap tree</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <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;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trees</span><span class="p">;</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nboot</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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29
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<pre style="margin: 0;">+<span id="LC29" 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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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur_edge</span><span class="p">;</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">hamming</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"> <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;">newtree</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// We compare the reference tree with the current bootstrap tree</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <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;">oldtrees</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trees</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trees</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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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <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;">oldname</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tree_name</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tree_name</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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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="n" style="color: #333;">free_tree</span><span class="p">(</span><span class="n" style="color: #333;">fd_boot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldtrees</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="n" style="color: #333;">fd_boot</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tree_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">oldname</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="n" style="color: #333;">mess</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">preptree</span><span class="p">(</span><span class="n" style="color: #333;">fd_boot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//TBE_PrintTree(fd_boot);</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mess</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="n" style="color: #333;">fl_alert</span><span class="p">(</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span> <span class="n" style="color: #333;">mess</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_branches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TBE_Assign_Branch_Ids</span><span class="p">(</span><span class="n" style="color: #333;">fd_boot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">Alloc_TBE_Matrices</span><span class="p">(</span><span class="n" style="color: #333;">fd_reftree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cluster_sizes</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_All_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">fd_reftree</span><span class="p">,</span> <span class="n" style="color: #333;">fd_boot</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_All_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">fd_reftree</span><span class="p">,</span> <span class="n" style="color: #333;">fd_boot</span><span class="p">,</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> </span>
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70
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<pre style="margin: 0;">+<span id="LC70" 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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fd_reftree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_edge</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_edge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">score</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">min_dist</span><span class="p">[</span><span class="n" style="color: #333;">cur_edge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_edge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">cur_edge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">];</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur_edge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="n" style="color: #333;">fd_reftree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span><span class="p">)){</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="n" style="color: #333;">cur_edge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fd_reftree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">cur_edge</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">p</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"> <span class="p">}</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="cpp"> <span class="p">}</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">Free_TBE_Matrices</span><span class="p">(</span><span class="n" style="color: #333;">fd_reftree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">cluster_sizes</span><span class="p">);</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="cpp"> <span class="n" style="color: #333;">nboot</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cpp"> <span class="n" style="color: #333;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">get_next_tree</span><span class="p">(</span><span class="n" style="color: #333;">fd_boot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="p">}</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">ref_branches</span><span class="p">);</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="cpp"> <span class="n" style="color: #333;">newtree</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="mi" style="color: #099;">500000</span><span class="p">);</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_PrintTree</span><span class="p">(</span><span class="n" style="color: #333;">newtree</span><span class="p">,</span><span class="n" style="color: #333;">fd_reftree</span><span class="p">,</span><span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">nboot</span><span class="p">);</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">reftree</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">newtree</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="cpp"><span class="p">}</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//////</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* Matrices used in transfer bootstrap computation (tbe.c) */</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Alloc_TBE_Matrices</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n_otu</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">){</span></span>
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98
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<pre style="margin: 0;">+<span id="LC98" 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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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_edges</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n_otu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">min_dist</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nb_edges</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* array of min Hamming distances */</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">min_dist_edge</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nb_edges</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* array of edge ids corresponding to min Hamming distances */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cluster_sizes</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nb_edges</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* array of sizes of clusters associated to each branch (in the post order traversal) */</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">c_matrix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nb_edges</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* matrix of cardinals of complements */</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i_matrix</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nb_edges</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* matrix of cardinals of intersections */</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hamming</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nb_edges</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">));</span> <span class="cm" style="color: #998; font-style: italic;">/* matrix of Hamming distances */</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" 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;">nb_edges</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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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">c_matrix</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nb_edges</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i_matrix</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nb_edges</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hamming</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">nb_edges</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="p">));</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">min_dist</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;">n_otu</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* initialization to the nb of taxa */</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cluster_sizes</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="mi" style="color: #099;">0</span><span class="p">;</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="cpp"> <span class="p">}</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="cpp"><span class="p">}</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="cpp"></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Free_TBE_Matrices</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n_otu</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" 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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<td class="diff-line-num new new_line" data-linenumber="119" 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">
119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb_edges</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n_otu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" 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;">nb_edges</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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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">c_matrix</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i_matrix</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hamming</span><span class="p">)[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="cpp"> <span class="p">}</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">c_matrix</span><span class="p">));</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">i_matrix</span><span class="p">));</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hamming</span><span class="p">));</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">min_dist</span><span class="p">));</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">min_dist_edge</span><span class="p">));</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cluster_sizes</span><span class="p">));</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"><span class="p">}</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="cpp"></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">///// Distance computation</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="cpp"></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/* UNION AND INTERSECT CALCULATIONS (FOR THE TRANSFER METHOD) */</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Update_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">orig</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">my_br</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_tree</span><span class="p">,</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_branches</span><span class="p">,</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_branches</span><span class="p">){</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* this function does the post-order traversal (recursive from the pseudoroot to the leaves, updating knowledge for the subtrees)</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> of the reference tree, examining only leaves (terminal edges) of the bootstrap tree.</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> It sends a probe from the orig node to the target node (nodes in ref_tree), calculating I_ij and C_ij</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> (see Brehelin, Gascuel, Martin 2008). */</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</span><span class="p">;</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">edge_id</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* its id */</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">next_edge_id</span><span class="p">;</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tip</span><span class="p">;</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">boot_edge_id</span><span class="p">;</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">my_br</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* all this is in ref_tree */</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="cpp"></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// A tip</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">))</span> <span class="p">{</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="cpp"> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</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>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* for all the terminal edges of boot_tree */</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If not tip, continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="158" 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">
158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">tip</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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<td class="diff-line-num new new_line" data-linenumber="159" 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">
159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bouta</span><span class="p">))</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="cpp"> <span class="n" style="color: #333;">tip</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bouta</span><span class="p">;</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">boutb</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="162" 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">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="cpp"> <span class="n" style="color: #333;">tip</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">boutb</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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">
163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">tip</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* we only want to scan terminal edges of boot_tree, where the right son is a leaf */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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">
165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* else we update all the I_ij and C_ij with i = edge_id */</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strcmp</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">labels</span><span class="p">[</span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rank</span><span class="p">],</span><span class="n" style="color: #333;">boot_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">labels</span><span class="p">[</span><span class="n" style="color: #333;">tip</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rank</span><span class="p">]))</span> <span class="p">{</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* here the taxa are different */</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</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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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="cpp"> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</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>
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170
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<pre style="margin: 0;">+<span id="LC170" 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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<td class="diff-line-num new new_line" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* same taxa here in T_ref and T_boot */</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</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>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</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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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end for on all edges of T_boot, for my_br being terminal */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" 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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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">]</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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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* now the case where my_br is not a terminal edge */</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* first initialise (zero) the cells we are going to update */</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">){</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* We initialize the i and c matrices for the edge edge_id with :</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * 0 for i : because afterwards we do i[edge_id] = i[edge_id] || i[next_edge_id]</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * 1 for c : because afterwards we do c[edge_id] = c[edge_id] && c[next_edge_id]</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bouta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">boutb</span><span class="p">)){</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</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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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</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>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="cpp"> <span class="p">}</span></span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="cpp"> <span class="p">}</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">orig</span><span class="p">){</span></span>
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<td class="diff-line-num new new_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id1</span><span class="p">]),</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="n" style="color: #333;">next_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id1</span><span class="p">;</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">next_edge_id</span><span class="p">];</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* for all the terminal edges of boot_tree */</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="197" 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">
197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If not a tip, continue</span></span>
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<td class="diff-line-num new new_line" data-linenumber="198" 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">
198
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<pre style="margin: 0;">+<span id="LC198" 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;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bouta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">boutb</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 new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">next_edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">];</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* above is an OR between two integers, result is 0 or 1 */</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="cpp"> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">next_edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">];</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* above is an AND between two integers, result is 0 or 1 */</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end for j */</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="cpp"> <span class="p">}</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">orig</span><span class="p">){</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span><span class="p">]),</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">next_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span><span class="p">;</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">next_edge_id</span><span class="p">];</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* for all the terminal edges of boot_tree */</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If not a tip, continue</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" 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;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bouta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">boutb</span><span class="p">))</span> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">next_edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* above is an OR between two integers, result is 0 or 1 */</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="cpp"> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">next_edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="216" 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="LC216" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* above is an AND between two integers, result is 0 or 1 */</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end for j */</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">orig</span><span class="p">){</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id3</span><span class="p">]),</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">next_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id3</span><span class="p">;</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">next_edge_id</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">;</span> <span class="n" style="color: #333;">j</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* for all the terminal edges of boot_tree */</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">boot_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// If not a tip, continue</span></span>
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<pre style="margin: 0;">+<span id="LC227" 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;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">bouta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">j</span><span class="p">].</span><span class="n" style="color: #333;">boutb</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="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">next_edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* above is an OR between two integers, result is 0 or 1 */</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">next_edge_id</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* above is an AND between two integers, result is 0 or 1 */</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end for j */</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* ending the case where my_br is an internal edge */</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"><span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end update_i_c_post_order_ref_tree */</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Update_All_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">boot_tree</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;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_branches</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_branches</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* this function is the first step of the union and intersection calculations */</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">root</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC244" 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;">ref_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id1</span><span class="p">]),</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span><span class="p">]),</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"><span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end update_all_i_c_post_order_ref_tree */</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Update_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">orig</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">target</span><span class="p">,</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">my_br</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span></span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_branches</span><span class="p">,</span></span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_branches</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* here we implement the second part of the Brehelin/Gascuel/Martin algorithm:</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> post-order traversal of the bootstrap tree, and numerical recurrence. </span></span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> in this function, orig and target are nodes of boot_tree (aka T_boot).</span></span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> min_dist is an array whose size is equal to the number of edges in T_ref.</span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> It gives for each edge of T_ref its min distance to a split in T_boot. */</span></span>
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<pre style="margin: 0;">+<span id="LC260" 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="LC261" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">boot_edge_id</span> <span class="cm" style="color: #998; font-style: italic;">/* its id */</span><span class="p">,</span> <span class="n" style="color: #333;">next_boot_edge_id</span> <span class="cm" style="color: #998; font-style: italic;">/* id of descending branches. */</span><span class="p">;</span></span>
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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;">int</span> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ref_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* we first have to determine which is the direction of the edge (orig -> target and target -> orig) */</span></span>
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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;">boot_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">my_br</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">id</span><span class="p">;</span> <span class="cm" style="color: #998; font-style: italic;">/* here this is an edge_id corresponding to T_boot */</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Not a taxon</span></span>
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267
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<pre style="margin: 0;">+<span id="LC267" 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;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">target</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="cm" style="color: #998; font-style: italic;">/* because nothing to do in the case where target is a leaf: intersection and union already ok. */</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* otherwise, keep on posttraversing in all other directions */</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="cpp"> </span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* first initialise (zero) the cells we are going to update */</span></span>
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272
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<pre style="margin: 0;">+<span id="LC272" 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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</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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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="cpp"> </span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">orig</span><span class="p">){</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">next_boot_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id1</span><span class="p">;</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">next_boot_edge_id</span><span class="p">]),</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" 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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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 class="cm" style="color: #998; font-style: italic;">/* for all the edges of ref_tree */</span> </span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">next_boot_edge_id</span><span class="p">];</span></span>
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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="cpp"> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">next_boot_edge_id</span><span class="p">];</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end for i */</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <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;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">orig</span><span class="p">){</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">next_boot_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" 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">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">next_boot_edge_id</span><span class="p">]),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" 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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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 class="cm" style="color: #998; font-style: italic;">/* for all the edges of ref_tree */</span> </span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">next_boot_edge_id</span><span class="p">];</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">next_boot_edge_id</span><span class="p">];</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end for i */</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="292" 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">
292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">orig</span><span class="p">){</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">next_boot_edge_id</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id3</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="294" 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">
294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">next_boot_edge_id</span><span class="p">]),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="295" 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">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="296" 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">
296
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<pre style="margin: 0;">+<span id="LC296" 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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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 class="cm" style="color: #998; font-style: italic;">/* for all the edges of ref_tree */</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="297" 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">
297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">next_boot_edge_id</span><span class="p">];</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">next_boot_edge_id</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="299" 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">
299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end for i */</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="301" 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">
301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end if target is not a leaf: the following loop is performed in all cases */</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="303" 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">
303
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<pre style="margin: 0;">+<span id="LC303" 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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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 class="cm" style="color: #998; font-style: italic;">/* for all the edges of ref_tree */</span> </span>
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<td class="diff-line-num new new_line" data-linenumber="304" 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">
304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* at this point we can calculate in all cases (internal branch or not) the Hamming distance at [i][boot_edge_id], */</span></span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* card of union minus card of intersection */</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="cpp"> <span class="n" style="color: #333;">hamming</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="cpp"> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="cm" style="color: #998; font-style: italic;">/* #taxa in the cluster i of T_ref */</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="cm" style="color: #998; font-style: italic;">/* #taxa in cluster edge_id of T_boot BUT NOT in cluster i of T_ref */</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">];</span> <span class="cm" style="color: #998; font-style: italic;">/* #taxa in the intersection of the two clusters */</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="cpp"> </span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* Let's immediately calculate the right ditance, taking into account the fact that the true disance is min (dist, N-dist) */</span></span>
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312
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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;">hamming</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">N</span><span class="o" style="font-weight: 600;">/</span><span class="mi" style="color: #099;">2</span> <span class="cm" style="color: #998; font-style: italic;">/* floor value */</span><span class="p">)</span> <span class="n" style="color: #333;">hamming</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">N</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">hamming</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">];</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* and update the min of all Hamming (TRANSFER) distances hamming[i][j] over all j */</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">hamming</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_dist</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]){</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dist</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;">hamming</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">boot_edge_id</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="cpp"> <span class="n" style="color: #333;">min_dist_edge</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;">boot_edge_id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp"> <span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end for on all edges of T_ref */</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp"><span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end update_i_c_post_order_boot_tree */</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp"></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Update_All_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_branches</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_branches</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* this function is the second step of the union and intersection calculations */</span></span>
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<pre style="margin: 0;">+<span id="LC329" 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="LC330" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">root</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC331" 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;">boot_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id1</span><span class="p">]),</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="cpp"> <span class="n" style="color: #333;">Update_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="p">,</span> <span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="p">(</span><span class="n" style="color: #333;">boot_branches</span><span class="p">[</span><span class="n" style="color: #333;">root</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span><span class="p">]),</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span> <span class="n" style="color: #333;">ref_branches</span><span class="p">,</span> <span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="cpp"> </span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/* and then some checks to make sure everything went ok */</span></span>
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<pre style="margin: 0;">+<span id="LC336" 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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">min_dist</span><span class="p">[</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">]</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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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">bouta</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">boutb</span><span class="p">)){</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</span><span class="p">(</span><span class="n" style="color: #333;">min_dist</span><span class="p">[</span><span class="n" style="color: #333;">ref_branches</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">id</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span> <span class="cm" style="color: #998; font-style: italic;">/* any terminal edge should have an exact match in any bootstrap tree */</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="cpp"><span class="p">}</span> <span class="cm" style="color: #998; font-style: italic;">/* end update_all_i_c_post_order_boot_tree */</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Assigns identifiers to all branches of the tree</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// And sets branch ids to each nodes br_id1 br_id2 and br_id3</span></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="cpp"><span class="n" style="color: #333;">TBE_Branch</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">TBE_Assign_Branch_Ids</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tree</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">branches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">TBE_Branch</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span> <span class="n" style="color: #333;">malloc</span><span class="p">((</span><span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</span><span class="p">)</span><span class="o" style="font-weight: 600;">*</span><span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Branch</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC350" 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;">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="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">notu</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">2</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="LC351" class="line" lang="cpp"> <span class="n" style="color: #333;">branches</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">score</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="LC352" class="line" lang="cpp"> <span class="n" style="color: #333;">branches</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">p</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="LC353" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Init_Branches</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;">racine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</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;">racine</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">id</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Init_Branches</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;">racine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</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;">racine</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">id</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">branches</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">TBE_Init_Branches</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">)</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="cpp"> <span class="n" style="color: #333;">branches</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">id</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="cpp"> <span class="n" style="color: #333;">branches</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">bouta</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prev</span><span class="p">;</span></span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">branches</span><span class="p">[</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">].</span><span class="n" style="color: #333;">boutb</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur</span><span class="p">;</span></span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="cpp"></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">prev</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="p">){</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">prev</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">prev</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="p">){</span></span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="cpp"> <span class="n" style="color: #333;">prev</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">prev</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="p">){</span></span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="cpp"> <span class="n" style="color: #333;">prev</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id3</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="cpp"> <span class="p">}</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="cpp"></span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="p">){</span></span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="cpp"> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id1</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="p">){</span></span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="cpp"> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="cpp"> <span class="p">}</span><span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="p">){</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id3</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="cpp"> <span class="p">}</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> </span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">prev</span><span class="p">){</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Init_Branches</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span><span class="n" style="color: #333;">id</span><span class="p">);</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="cpp"> <span class="p">}</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">prev</span><span class="p">){</span></span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Init_Branches</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span><span class="n" style="color: #333;">id</span><span class="p">);</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="cpp"> <span class="p">}</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">!=</span><span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">prev</span><span class="p">){</span></span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_Init_Branches</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span><span class="n" style="color: #333;">id</span><span class="p">);</span></span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="cpp"> <span class="p">}</span></span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="cpp"><span class="p">}</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</span><span class="p">){</span></span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nneigh</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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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">nneigh</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</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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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="cpp"> <span class="n" style="color: #333;">nneigh</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</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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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">nneigh</span><span class="o" style="font-weight: 600;">+=</span><span class="p">(</span><span class="n" style="color: #333;">n</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</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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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">nneigh</span><span class="o" style="font-weight: 600;">==</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="cpp"><span class="p">}</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="cpp"></span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">TBE_PrintTree</span><span class="p">(</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;">nwstring</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nboot</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">pos</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="LC403" class="line" lang="cpp"> <span class="n" style="color: #333;">nwstring</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'('</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_PrintTree_Recur</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nwstring</span><span class="p">,</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="p">,</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id1</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l1</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="n" style="color: #333;">nboot</span><span class="p">);</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="cpp"> <span class="n" style="color: #333;">nwstring</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">','</span><span class="p">;</span></span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_PrintTree_Recur</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nwstring</span><span class="p">,</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="p">,</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span><span class="p">,</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">racine</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l2</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="n" style="color: #333;">nboot</span><span class="p">);</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="n" style="color: #333;">nwstring</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">')'</span><span class="p">;</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">nwstring</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">';'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">nwstring</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">++</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">TBE_PrintTree_Recur</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</span><span class="p">,</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;">nwstring</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur</span><span class="p">,</span><span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">orig</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cur_edge</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nboot</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="p">)){</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</span><span class="p">)</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">nwstring</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;">pos</span><span class="p">),</span><span class="mi" style="color: #099;">500000</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;">pos</span><span class="p">),</span><span class="s" style="color: #d14;">"%s"</span><span class="p">,</span><span class="n" style="color: #333;">t</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">labels</span><span class="p">[</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">rank</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC415" 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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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">nwstring</span><span class="p">[(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</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="sc" style="color: #d14;">'('</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nb</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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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">orig</span><span class="p">){</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_PrintTree_Recur</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">nwstring</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v1</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id1</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l1</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="n" style="color: #333;">nboot</span><span class="p">);</span></span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">nb</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="cpp"> <span class="p">}</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">orig</span><span class="p">){</span></span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">nb</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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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">nwstring</span><span class="p">[(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</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="sc" style="color: #d14;">','</span><span class="p">;</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_PrintTree_Recur</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">nwstring</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v2</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l2</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="n" style="color: #333;">nboot</span><span class="p">);</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="cpp"> <span class="n" style="color: #333;">nb</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="p">}</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="o" style="font-weight: 600;">!=</span><span class="n" style="color: #333;">orig</span><span class="p">){</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="cpp"> <span class="n" style="color: #333;">nwstring</span><span class="p">[(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</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="sc" style="color: #d14;">','</span><span class="p">;</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">TBE_PrintTree_Recur</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nwstring</span><span class="p">,</span> <span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">v3</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">br_id2</span><span class="p">,</span> <span class="n" style="color: #333;">cur</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">l3</span><span class="p">,</span> <span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="n" style="color: #333;">nboot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="cpp"> <span class="p">}</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="cpp"> <span class="n" style="color: #333;">nwstring</span><span class="p">[(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</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="sc" style="color: #d14;">')'</span><span class="p">;</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="cpp"></span>
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434
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Compute and write support</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">branches</span><span class="p">[</span><span class="n" style="color: #333;">cur_edge</span><span class="p">].</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">></span><span class="mi" style="color: #099;">1</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">support</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">100.0</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">branches</span><span class="p">[</span><span class="n" style="color: #333;">cur_edge</span><span class="p">].</span><span class="n" style="color: #333;">score</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">1.0</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">nboot</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span><span class="n" style="color: #333;">branches</span><span class="p">[</span><span class="n" style="color: #333;">cur_edge</span><span class="p">].</span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</span><span class="p">)</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">nwstring</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;">pos</span><span class="p">),</span><span class="mi" style="color: #099;">500000</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;">pos</span><span class="p">),</span><span class="s" style="color: #d14;">"%d"</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">(</span><span class="n" style="color: #333;">support</span><span class="o" style="font-weight: 600;">+</span><span class="mf" style="color: #099;">0.5</span><span class="p">));</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Write length</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="cpp"> <span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</span><span class="p">)</span><span class="o" style="font-weight: 600;">+=</span><span class="n" style="color: #333;">snprintf</span><span class="p">(</span><span class="n" style="color: #333;">nwstring</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;">pos</span><span class="p">),</span><span class="mi" style="color: #099;">500000</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;">pos</span><span class="p">),</span><span class="s" style="color: #d14;">":%f"</span><span class="p">,</span><span class="n" style="color: #333;">length</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#2be9eda7c11e18a541fd58e783a923efa38e8ff3"><strong>tbe.h</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#ifndef TBE_H</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define TBE_H</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "treedraw.h"</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Main function for computing TBE support</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> - reftree: 1 tree in newick string</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> - boottrees: several trees in a single newick string</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;"> - returns: newick string of the tree with supports</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="c"><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;">TBE_Compute</span><span class="p">(</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;">reftree</span><span class="p">,</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;">boottrees</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="p">{</span> <span class="cm" style="color: #998; font-style: italic;">/* une branche definie par ses deux extremites */</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">noeud</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bouta</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">noeud</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boutb</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="c"> <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;">br_label</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">id</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">score</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// For TBE bootstrap support</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">p</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// Number of taxa on the light side og the bipartition (only defined after TBE_Bootstrap)</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"><span class="p">}</span> <span class="n" style="color: #333;">TBE_Branch</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">FD_nj_plot</span> <span class="n" style="color: #333;">TBE_Tree</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="c"><span class="k" style="font-weight: 600;">typedef</span> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">noeud</span> <span class="n" style="color: #333;">TBE_Node</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Matrices used in transfer bootstrap computation (tbe.c) */</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Alloc_TBE_Matrices</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n_otu</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span><span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Free_TBE_Matrices</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">n_otu</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">***</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="c"><span class="cm" style="color: #998; font-style: italic;">/* Transfer distance computation */</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Update_All_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="c"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_branches</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="c"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Update_IC_Ref_Tree</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">orig</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">target</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">my_br</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_tree</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="c"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_branches</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="c"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Update_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">orig</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">target</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="c"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">my_br</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="c"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_branches</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="c"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">Update_All_IC_Boot_Tree</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">ref_tree</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">boot_tree</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i_matrix</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">c_matrix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">hamming</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">short</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">min_dist_edge</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">cluster_sizes</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="c"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ref_branches</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">boot_branches</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// Assigns identifiers to all TBE_branchs of the tree</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">// And sets branch ids to each nodes br_id1 br_id2 and br_id3</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"><span class="n" style="color: #333;">TBE_Branch</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">TBE_Assign_Branch_Ids</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">tree</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">TBE_Init_Branches</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">id</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">TBE_Is_Taxon</span><span class="p">(</span><span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">n</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">TBE_PrintTree</span><span class="p">(</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;">nwstring</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nboot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">TBE_PrintTree_Recur</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pos</span><span class="p">,</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;">nwstring</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Tree</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">t</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">cur</span><span class="p">,</span><span class="n" style="color: #333;">TBE_Node</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">orig</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">cur_edge</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">TBE_Branch</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">branches</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">nboot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span></pre>
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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">@@ -16,6 +16,9 @@ struct noeud {</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">noeud</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v1</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v2</span><span class="p">,</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">v3</span><span class="p">;</span></span>
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="c"> <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;">nom</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">rank</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// Branches may be associated with id</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">// And this may be used in some cases</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">br_id1</span><span class="p">,</span> <span class="n" style="color: #333;">br_id2</span><span class="p">,</span> <span class="n" style="color: #333;">br_id3</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">nom</span> <span class="p">{</span></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">@@ -130,5 +133,7 @@ struct FD_nj_plot {</td>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"><span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC135" class="line" lang="c"><span class="k" style="font-weight: 600;">extern</span> <span class="n" style="color: #333;">Fl_Window</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">treedraw</span><span class="p">(</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</span><span class="p">,</span> <span class="n" style="color: #333;">SEA_VIEW</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">view</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;">name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">from_tree_menu</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"><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;">get_next_tree</span><span class="p">(</span><span class="n" style="color: #333;">FD_nj_plot</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fd_nj_plot</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">free_tree</span><span class="p">(</span><span class="n" style="color: #333;">FD_nj_plot</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fd_nj_plot</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif // TREEDRAW_H</span></span></pre>
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<a href="https://salsa.debian.org/med-team/seaview/compare/0ed3668bc2b7dbb24249c80df50f1604df520d13...b5aefb54f7e92027ac1e0776d4e13dea591aa77b#3bb2c0d8693fbdda425f55aff63ef52cf340505a"><strong>trees.cxx</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">@@ -3,6 +3,7 @@</td>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "seaview.h"</span></span>
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "treedraw.h"</span></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "tbe.h"</span></span>
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6
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <FL/Fl_Round_Button.H></span></span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <FL/Fl_Check_Button.H></span></span>
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8
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <FL/Fl_Select_Browser.H></span></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">@@ -43,7 +44,7 @@ void distance_method_dialog(SEA_VIEW *view);</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"><span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">run_calc_dist_matrix</span><span class="p">(</span><span class="n" style="color: #333;">allseq</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">distkind</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">protein</span><span class="p">,</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;">lwlseqs</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">in_bootstrap</span><span class="p">,</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;">p_err_mess</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">no_gui</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><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;">run_distance_method</span><span class="p">(</span><span class="n" style="color: #333;">SEA_VIEW</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">distkind</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">remove_all_gaps</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">use_bionj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">use_bootstrap</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">replicates</span><span class="p">,</span> <span class="n" style="color: #333;">Fl_Box</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">box</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;">distance_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">using_kaks</span><span class="p">,</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">distancefname</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">user_tree</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_gui</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="idiff"> </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">alert</span></span><span class="p"><span class="idiff">)(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">...),</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">keep_b_trees</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></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">distancefname</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">user_tree</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_gui</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="idiff"> </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">alert</span></span><span class="p"><span class="idiff">)(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">...),</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">keep_b_trees</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">compute_tbe</span></span> <span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="cpp"><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;">bootstrap_reformat</span><span class="p">(</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</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">replicates</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"><span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Obs_Dist</span><span class="p">(</span><span class="n" style="color: #333;">allseq</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">mod</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"><span class="n" style="color: #333;">matrix</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Kimura_p_Dist</span><span class="p">(</span><span class="n" style="color: #333;">allseq</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">data</span><span class="p">);</span></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">@@ -221,12 +222,17 @@ static void distance_callback(Fl_Widget *wgt, void *data)</td>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">dist_b_cb</span><span class="p">(</span><span class="n" style="color: #333;">Fl_Widget</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">wgt</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Button</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">buttons</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Fl_Button</span> <span class="o" style="font-weight: 600;">**</span><span class="p">)</span><span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">me</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Fl_Button</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">wgt</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">target</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Fl_Button</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">me</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">())</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">activate</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC229" class="line" lang="cpp"> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC227" 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;">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="mi" style="color: #099;">2</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="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">target</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">buttons</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">target</span><span class="p">){</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">me</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">())</span> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">activate</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="n" style="color: #333;">target</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="249" 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">@@ -249,10 +255,11 @@ void distance_method_dialog(SEA_VIEW *view)</td>
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249
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Fl_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">interrupt</span><span class="p">;</span></span>
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250
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Fl_Return_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">go</span><span class="p">;</span></span>
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251
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">started</span><span class="p">,</span> <span class="n" style="color: #333;">maxchoice</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC252" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Fl_Check_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">keep_b_trees</span><span class="p">;</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Fl_Check_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">keep_b_trees</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Fl_Check_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">compute_tbe</span><span class="p">;</span></span>
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253
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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;">if</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">)</span> <span class="p">{</span></span>
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254
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<td class="diff-line-num new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="cpp"> <span class="n" style="color: #333;">first</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">FALSE</span><span class="p">;</span></span>
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255
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<td class="diff-line-num new_line old" data-linenumber="262" 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="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Window</span><span class="p">(</span><span class="mi" style="color: #099;">2<span class="idiff left">50</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">240</span></span><span class="p">);</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">w</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Window</span><span class="p">(</span><span class="mi" style="color: #099;">2<span class="idiff left">70</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">265</span></span><span class="p">);</span></span>
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256
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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="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">label</span><span class="p">(</span><span class="s" style="color: #d14;">"Distance analysis"</span><span class="p">);</span></span>
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257
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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;">w</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">set_modal</span><span class="p">();</span></span>
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258
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<td class="diff-line-num new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"> <span class="n" style="color: #333;">nj</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Round_Button</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">60</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"NJ"</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="264" 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="271" 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">@@ -264,7 +271,7 @@ void distance_method_dialog(SEA_VIEW *view)</td>
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264
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<td class="diff-line-num new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"> <span class="n" style="color: #333;">distance</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Choice</span><span class="p">(</span><span class="mi" style="color: #099;">90</span><span class="p">,</span> <span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="mi" style="color: #099;">100</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"Distance"</span><span class="p">);</span></span>
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265
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<td class="diff-line-num new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="n" style="color: #333;">FL_ALIGN_LEFT</span><span class="p">);</span></span>
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266
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<td class="diff-line-num new_line" data-linenumber="273" 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">
273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="n" style="color: #333;">ignore_all_gaps</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Check_Button</span><span class="p">(</span><span class="mi" style="color: #099;">160</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">20</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="s" style="color: #d14;">"<span class="idiff left right">i</span>gnore all gap sites"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="268" 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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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="s" style="color: #d14;">"<span class="idiff left right">I</span>gnore all gap sites"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="268" 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">
268
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<td class="diff-line-num new_line" data-linenumber="275" 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">
275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">ignore_all_gaps</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="269" 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">
269
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<td class="diff-line-num new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="n" style="color: #333;">ignore_all_gaps</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="n" style="color: #333;">FL_ALIGN_LEFT</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="270" 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">
270
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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">
277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ignore_all_gaps</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">ignore_all_gaps</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">25</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="274" 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -274,10 +281,19 @@ void distance_method_dialog(SEA_VIEW *view)</td>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">tmp</span><span class="p">[</span><span class="mi" style="color: #099;">10</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="s" style="color: #d14;">"%d"</span><span class="p">,</span> <span class="n" style="color: #333;">def_replicates</span><span class="p">);</span></span>
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276
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">replicates</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">);</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">keep_b_trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Check_Button</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">bootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">180</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"Show bootstrap trees"</span><span class="p">);</span></span>
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278
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">keep_b_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</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="n" style="color: #333;">bootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">dist_b_cb</span><span class="p">,</span> <span class="n" style="color: #333;">keep_b_trees</span><span class="p">);</span></span>
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280
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<pre style="margin: 0;">-<span id="LC280" class="line" lang="cpp"> <span class="n" style="color: #333;">bootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">when</span><span class="p">(</span><span class="n" style="color: #333;">FL_WHEN_CHANGED</span><span class="p">);</span></span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="n" style="color: #333;">compute_tbe</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Check_Button</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">bootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">bootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">280</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"Transfer Bootstrap Expectation method"</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="cpp"> <span class="n" style="color: #333;">compute_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</span><span class="p">();</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"></span>
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<td class="diff-line-num new new_line" data-linenumber="288" 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">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="n" style="color: #333;">keep_b_trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Check_Button</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">compute_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">compute_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">180</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"Show bootstrap trees"</span><span class="p">);</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="n" style="color: #333;">keep_b_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</span><span class="p">();</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Fl_Check_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buttons</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">buttons</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="n" style="color: #333;">compute_tbe</span><span class="p">;</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"> <span class="n" style="color: #333;">buttons</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">keep_b_trees</span><span class="p">;</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp"> <span class="n" style="color: #333;">bootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">dist_b_cb</span><span class="p">,</span> <span class="n" style="color: #333;">buttons</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="295" 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">
295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp"> <span class="n" style="color: #333;">bootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">when</span><span class="p">(</span><span class="n" style="color: #333;">FL_WHEN_CHANGED</span><span class="p">);</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp"> </span>
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281
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297
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<pre style="margin: 0;"> <span id="LC297" class="line" lang="cpp"> <span class="n" style="color: #333;">box</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Box</span><span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">keep_b_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">keep_b_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">150</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">);</span></span>
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282
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298
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<pre style="margin: 0;"> <span id="LC298" class="line" lang="cpp"> <span class="n" style="color: #333;">usertree</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Round_Button</span><span class="p">(</span><span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span><span class="p">(),</span> <span class="n" style="color: #333;">box</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">box</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">15</span><span class="p">,</span> <span class="mi" style="color: #099;">85</span><span class="p">,</span> <span class="n" style="color: #333;">nj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">(),</span> <span class="s" style="color: #d14;">"User tree:"</span><span class="p">);</span></span>
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283
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299
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<pre style="margin: 0;"> <span id="LC299" class="line" lang="cpp"> <span class="n" style="color: #333;">usertree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">type</span><span class="p">(</span><span class="n" style="color: #333;">FL_RADIO_BUTTON</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="362" 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="378" 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">@@ -362,7 +378,7 @@ void distance_method_dialog(SEA_VIEW *view)</td>
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362
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378
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<pre style="margin: 0;"> <span id="LC378" class="line" lang="cpp"> <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</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">run_distance_method</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">distance_choice</span><span class="p">,</span> <span class="n" style="color: #333;">ignore_all_gaps</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">(),</span> <span class="n" style="color: #333;">bionj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">(),</span> </span>
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363
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<td class="diff-line-num new_line" data-linenumber="379" 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">
379
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<pre style="margin: 0;"> <span id="LC379" class="line" lang="cpp"> <span class="n" style="color: #333;">bootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">(),</span> <span class="n" style="color: #333;">def_replicates</span><span class="p">,</span> <span class="n" style="color: #333;">box</span><span class="p">,</span> <span class="n" style="color: #333;">distance</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">text</span><span class="p">(),</span> <span class="n" style="color: #333;">using_kaks</span><span class="p">,</span></span>
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364
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">savetofile</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">()</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="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="n" style="color: #333;">usertree</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">()</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">view</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">trees</span><span class="p">[</span><span class="n" style="color: #333;">treechoice</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">()]</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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365
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<td class="diff-line-num new_line old" data-linenumber="381" 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="LC365" class="line" lang="cpp"> <span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">false</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fl_alert</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">keep_b_trees</span></span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">());</span></span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="cpp"> <span class="idiff left"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">false</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fl_alert</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">keep_b_trees</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">(),</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">compute_tbe</span></span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">());</span></span>
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366
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382
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<pre style="margin: 0;"> <span id="LC382" 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;">choice</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bionj</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">()</span><span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"BioNJ_tree"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"NJ_tree"</span><span class="p">;</span></span>
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367
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383
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<pre style="margin: 0;"> <span id="LC383" 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;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extract_filename</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">masename</span><span class="p">);</span></span>
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368
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"> <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;">title</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="438" 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="454" 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">@@ -438,7 +454,7 @@ matrix *run_calc_dist_matrix(allseq *seqs, int distkind, int protein, char **lwl</td>
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438
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454
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<pre style="margin: 0;"> <span id="LC454" class="line" lang="cpp"></span>
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439
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455
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<pre style="margin: 0;"> <span id="LC455" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="nf" style="color: #900; font-weight: 600;">run_distance_method</span><span class="p">(</span><span class="n" style="color: #333;">SEA_VIEW</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">distkind</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">remove_all_gaps</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">use_bionj</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">use_bootstrap</span><span class="p">,</span></span>
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440
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456
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">replicates</span><span class="p">,</span> <span class="n" style="color: #333;">Fl_Box</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">box</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;">distance_name</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">using_kaks</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;">distancefname</span><span class="p">,</span></span>
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441
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<pre style="margin: 0;">-<span id="LC441" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">user_tree</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_gui</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="idiff"> </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">alert</span></span><span class="p"><span class="idiff">)(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">...),</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">keep_b_trees</span></span> <span class="p">)</span></span>
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457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="cpp"> <span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">user_tree</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">no_gui</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">void</span></span><span class="idiff"> </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">alert</span></span><span class="p"><span class="idiff">)(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="p"><span class="idiff">...),</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">keep_b_trees</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">int</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">compute_tbe</span></span> <span class="p">)</span></span>
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442
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="443" 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">
443
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<td class="diff-line-num new_line" data-linenumber="459" 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">
459
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<pre style="margin: 0;"> <span id="LC459" class="line" lang="cpp"> <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;">display_tree</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">bootstrap_trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">err_mess</span><span class="p">,</span> <span class="n" style="color: #333;">tree_label</span><span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">]</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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444
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460
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">total</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="p">,</span> <span class="n" style="color: #333;">j</span><span class="p">,</span> <span class="n" style="color: #333;">lbtrees</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="511" 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="527" 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">@@ -511,7 +527,7 @@ char *run_distance_method(SEA_VIEW *view, int distkind, int remove_all_gaps, int</td>
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511
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527
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<pre style="margin: 0;"> <span id="LC527" class="line" lang="cpp"> <span class="n" style="color: #333;">phyml_mat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Make_Tree_From_Scratch</span><span class="p">(</span><span class="n" style="color: #333;">phyml_seqs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_otu</span><span class="p">,</span> <span class="n" style="color: #333;">phyml_seqs</span><span class="p">);</span></span>
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512
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528
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<pre style="margin: 0;"> <span id="LC528" class="line" lang="cpp"> <span class="n" style="color: #333;">Bionj</span><span class="p">(</span><span class="n" style="color: #333;">phyml_mat</span><span class="p">);</span></span>
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513
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<td class="diff-line-num new_line" data-linenumber="529" 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">
529
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<pre style="margin: 0;"> <span id="LC529" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s %d sites %s"</span><span class="p">,</span> <span class="n" style="color: #333;">use_bionj</span> <span class="o" style="font-weight: 600;">?</span> <span class="s" style="color: #d14;">"BioNJ"</span> <span class="o" style="font-weight: 600;">:</span> <span class="s" style="color: #d14;">"NJ"</span><span class="p">,</span></span>
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514
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<td class="diff-line-num new_line old" data-linenumber="530" 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="LC514" class="line" lang="cpp"> <span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff">phyml_seqs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">clean_len</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">distance_name</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">phyml_seqs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">clean_len</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">distance_name</span></span><span class="p">);</span></span>
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515
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531
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<pre style="margin: 0;"> <span id="LC531" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">use_bootstrap</span><span class="p">)</span> <span class="p">{</span></span>
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516
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532
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<pre style="margin: 0;"> <span id="LC532" class="line" lang="cpp"> <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;">full_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Write_Tree</span><span class="p">(</span><span class="n" style="color: #333;">phyml_mat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tree</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="517" 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">
517
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533
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<pre style="margin: 0;"> <span id="LC533" class="line" lang="cpp"> <span class="n" style="color: #333;">Free_Tree</span><span class="p">(</span><span class="n" style="color: #333;">phyml_mat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tree</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="532" 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="548" 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">@@ -532,7 +548,7 @@ char *run_distance_method(SEA_VIEW *view, int distkind, int remove_all_gaps, int</td>
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532
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548
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<pre style="margin: 0;"> <span id="LC548" class="line" lang="cpp"> <span class="n" style="color: #333;">phyml_mat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Make_Tree_From_Scratch</span><span class="p">(</span><span class="n" style="color: #333;">phyml_seqs</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">n_otu</span><span class="p">,</span> <span class="n" style="color: #333;">phyml_seqs</span><span class="p">);</span></span>
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533
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549
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<pre style="margin: 0;"> <span id="LC549" class="line" lang="cpp"> <span class="n" style="color: #333;">Bionj</span><span class="p">(</span><span class="n" style="color: #333;">phyml_mat</span><span class="p">);</span></span>
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534
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<td class="diff-line-num new_line" data-linenumber="550" 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">
550
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<pre style="margin: 0;"> <span id="LC550" class="line" lang="cpp"> <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;">one_replicate_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Write_Tree</span><span class="p">(</span><span class="n" style="color: #333;">phyml_mat</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tree</span><span class="p">);</span></span>
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535
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<pre style="margin: 0;">-<span id="LC535" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">keep_b_trees</span><span class="p">)</span> <span class="p">{</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">keep_b_trees</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">compute_tbe</span></span><span class="p">)</span> <span class="p">{</span></span>
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536
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<td class="diff-line-num new_line" data-linenumber="552" 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">
552
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<pre style="margin: 0;"> <span id="LC552" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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537
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<td class="diff-line-num new_line" data-linenumber="553" 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">
553
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<pre style="margin: 0;"> <span id="LC553" class="line" lang="cpp"> <span class="n" style="color: #333;">lbtrees</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">replicates</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">one_replicate_tree</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>
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538
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554
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<pre style="margin: 0;"> <span id="LC554" class="line" lang="cpp"> <span class="n" style="color: #333;">bootstrap_trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">lbtrees</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="564" 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="580" 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">@@ -564,7 +580,7 @@ char *run_distance_method(SEA_VIEW *view, int distkind, int remove_all_gaps, int</td>
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564
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<td class="diff-line-num new_line" data-linenumber="580" 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">
580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="565" 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">
565
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<td class="diff-line-num new_line" data-linenumber="581" 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">
581
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<pre style="margin: 0;"> <span id="LC581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="566" 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">
566
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582
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<pre style="margin: 0;"> <span id="LC582" class="line" lang="cpp"> <span class="n" style="color: #333;">display_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">finish_add_bootstrap</span><span class="p">(</span><span class="n" style="color: #333;">total</span><span class="p">);</span></span>
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567
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<pre style="margin: 0;">-<span id="LC567" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">),</span> <span class="s" style="color: #d14;">" %d repl.<span class="idiff left">"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">total</span></span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="568" 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="583" 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">
583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">),</span> <span class="s" style="color: #d14;">" %d repl.<span class="idiff left">%s"</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">total</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">compute_tbe</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">" (TBE)"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">""</span></span><span class="idiff right"> </span><span class="p">);</span></span>
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568
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<td class="diff-line-num new_line" data-linenumber="584" 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">
584
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<pre style="margin: 0;"> <span id="LC584" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="569" 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">
569
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<td class="diff-line-num new_line" data-linenumber="585" 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">
585
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<pre style="margin: 0;"> <span id="LC585" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">display_tree</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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570
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586
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<pre style="margin: 0;"> <span id="LC586" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="581" 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="597" 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">@@ -581,12 +597,15 @@ char *run_distance_method(SEA_VIEW *view, int distkind, int remove_all_gaps, int</td>
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581
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<td class="diff-line-num new_line" data-linenumber="597" 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">
597
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<pre style="margin: 0;"> <span id="LC597" 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;">using_kaks</span><span class="p">)</span> <span class="n" style="color: #333;">alert</span><span class="p">(</span><span class="s" style="color: #d14;">"Can't compute distances because sequences are too divergent.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Are they aligned?"</span><span class="p">);</span></span>
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582
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<td class="diff-line-num new_line" data-linenumber="598" 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">
598
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<pre style="margin: 0;"> <span id="LC598" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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583
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599
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<pre style="margin: 0;"> <span id="LC599" class="line" lang="cpp"> <span class="p">}</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bootstrap_trees</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">compute_tbe</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="601" 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">
601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"> <span class="n" style="color: #333;">display_tree</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">TBE_Compute</span><span class="p">(</span><span class="n" style="color: #333;">display_tree</span><span class="p">,</span><span class="n" style="color: #333;">bootstrap_trees</span><span class="p">);</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"> <span class="p">}</span></span>
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584
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603
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//add label to tree</span></span>
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<td class="diff-line-num old_line" data-linenumber="585" 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">
585
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<td class="diff-line-num new_line" data-linenumber="604" 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">
604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="cpp"> <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</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">display_tree</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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586
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="s" style="color: #d14;">"[%s] %s"</span><span class="p">,</span> <span class="n" style="color: #333;">tree_label</span><span class="p">,</span> <span class="n" style="color: #333;">display_tree</span><span class="p">);</span></span>
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587
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606
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<pre style="margin: 0;"> <span id="LC606" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">display_tree</span><span class="p">);</span></span>
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588
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">box</span><span class="p">)</span> <span class="n" style="color: #333;">box</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">window</span><span class="p">()</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">hide</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//necessary under X11 so tree is in foreground</span></span>
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589
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<pre style="margin: 0;">-<span id="LC589" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bootstrap_trees</span><span class="p">)</span> <span class="p">{</span></span>
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608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">bootstrap_trees</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">keep_b_trees</span></span><span class="p">)</span> <span class="p">{</span></span>
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590
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="cpp"> <span class="n" style="color: #333;">treedraw</span><span class="p">(</span><span class="n" style="color: #333;">bootstrap_trees</span><span class="p">,</span> <span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="s" style="color: #d14;">"bootstrap trees"</span><span class="p">,</span> <span class="n" style="color: #333;">FALSE</span><span class="p">);</span></span>
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591
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610
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<pre style="margin: 0;"> <span id="LC610" class="line" lang="cpp"> <span class="p">}</span></span>
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592
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611
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<pre style="margin: 0;"> <span id="LC611" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tree</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="733" 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="752" 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">@@ -733,17 +752,21 @@ Fl_Round_Button *g_no; Fl_Choice *g_cats; Fl_Round_Button *a_est; Fl_Float_Input</td>
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733
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<td class="diff-line-num new_line" data-linenumber="752" 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">
752
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<pre style="margin: 0;"> <span id="LC752" class="line" lang="cpp"><span class="n" style="color: #333;">Fl_Round_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nni_b</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">spr_b</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">nni_spr_b</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="734" 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">
734
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<td class="diff-line-num new_line" data-linenumber="753" 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">
753
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<pre style="margin: 0;"> <span id="LC753" class="line" lang="cpp"><span class="n" style="color: #333;">Fl_Round_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u_bionj</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u_menutree</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u_random</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="735" 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">
735
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<td class="diff-line-num new_line" data-linenumber="754" 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">
754
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<pre style="margin: 0;"> <span id="LC754" class="line" lang="cpp"><span class="n" style="color: #333;">Fl_Choice</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u_choice</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="736" 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">
736
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<td class="diff-line-num new_line old" data-linenumber="755" 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="LC736" class="line" lang="cpp"><span class="n" style="color: #333;">Fl_Check_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u_optimize</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u_quiet</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b_keep_trees</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="737" 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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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="cpp"><span class="n" style="color: #333;">Fl_Check_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u_optimize</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u_quiet</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b_keep_trees</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">b_tbe</span></span><span class="p">;</span></span>
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737
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756
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<pre style="margin: 0;"> <span id="LC756" class="line" lang="cpp"><span class="n" style="color: #333;">Fl_Int_Input</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">u_random_count</span><span class="p">;</span></span>
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738
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757
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<pre style="margin: 0;"> <span id="LC757" class="line" lang="cpp"><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;">phyml_path</span><span class="p">;</span></span>
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739
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="cpp"></span>
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740
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759
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">support_cb</span><span class="p">(</span><span class="n" style="color: #333;">Fl_Widget</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">wid</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">data</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="741" 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">
741
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="742" 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">
742
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<td class="diff-line-num new_line" data-linenumber="761" 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">
761
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<pre style="margin: 0;"> <span id="LC761" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">Fl_Button</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="743" 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">
743
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<pre style="margin: 0;">-<span id="LC743" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">())</span> <span class="n" style="color: #333;">b_keep_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">activate</span><span class="p">();</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">())</span> <span class="p">{</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="cpp"> <span class="n" style="color: #333;">b_keep_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">activate</span><span class="p">();</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="cpp"> <span class="n" style="color: #333;">b_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">activate</span><span class="p">();</span></span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="744" 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">
744
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<td class="diff-line-num new_line" data-linenumber="766" 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">
766
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<pre style="margin: 0;"> <span id="LC766" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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745
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767
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<pre style="margin: 0;"> <span id="LC767" class="line" lang="cpp"> <span class="n" style="color: #333;">b_keep_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</span><span class="p">();</span></span>
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746
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768
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<pre style="margin: 0;"> <span id="LC768" class="line" lang="cpp"> <span class="n" style="color: #333;">b_keep_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="cpp"> <span class="n" style="color: #333;">b_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</span><span class="p">();</span></span>
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747
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770
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<pre style="margin: 0;"> <span id="LC770" class="line" lang="cpp"> <span class="p">}</span></span>
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748
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771
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<pre style="margin: 0;"> <span id="LC771" class="line" lang="cpp"><span class="p">}</span></span>
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749
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="831" 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">@@ -831,7 +854,7 @@ void phyml_dialog(SEA_VIEW *view)</td>
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831
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854
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<pre style="margin: 0;"> <span id="LC854" class="line" lang="cpp"> <span class="p">}</span></span>
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832
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855
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<pre style="margin: 0;"> <span id="LC855" class="line" lang="cpp"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">mymodel</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">25</span><span class="p">;</span></span>
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833
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856
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<pre style="margin: 0;"> <span id="LC856" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//bootstrap</span></span>
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834
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<pre style="margin: 0;">-<span id="LC834" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Group</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Group</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">w</span><span class="p">(),</span> <span class="mi" style="color: #099;"><span class="idiff left right">7</span>5</span><span class="p">,</span> <span class="s" style="color: #d14;">"Branch Support"</span><span class="p">);</span></span>
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857
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<pre style="margin: 0;">+<span id="LC857" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Group</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">b_group</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Group</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">w</span><span class="p">(),</span> <span class="mi" style="color: #099;"><span class="idiff left right">9</span>5</span><span class="p">,</span> <span class="s" style="color: #d14;">"Branch Support"</span><span class="p">);</span></span>
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835
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858
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<pre style="margin: 0;"> <span id="LC858" class="line" lang="cpp"> <span class="n" style="color: #333;">b_group</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">box</span><span class="p">(</span><span class="n" style="color: #333;">FL_ROUNDED_BOX</span><span class="p">);</span></span>
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836
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859
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<pre style="margin: 0;"> <span id="LC859" class="line" lang="cpp"> <span class="n" style="color: #333;">b_group</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="n" style="color: #333;">FL_ALIGN_TOP</span><span class="o" style="font-weight: 600;">|</span><span class="n" style="color: #333;">FL_ALIGN_CENTER</span><span class="p">);</span></span>
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837
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860
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<pre style="margin: 0;"> <span id="LC860" class="line" lang="cpp"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="846" 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="869" 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">@@ -846,9 +869,14 @@ void phyml_dialog(SEA_VIEW *view)</td>
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846
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869
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<pre style="margin: 0;"> <span id="LC869" class="line" lang="cpp"> <span class="n" style="color: #333;">b_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Int_Input</span><span class="p">(</span><span class="n" style="color: #333;">b_yes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">b_yes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">w</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="mi" style="color: #099;">50</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"replicates"</span><span class="p">);</span></span>
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847
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870
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<pre style="margin: 0;"> <span id="LC870" class="line" lang="cpp"> <span class="n" style="color: #333;">b_count</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="n" style="color: #333;">FL_ALIGN_RIGHT</span><span class="p">);</span></span>
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848
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871
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<pre style="margin: 0;"> <span id="LC871" class="line" lang="cpp"> <span class="n" style="color: #333;">b_count</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">static_value</span><span class="p">(</span><span class="s" style="color: #d14;">"100"</span><span class="p">);</span></span>
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872
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<pre style="margin: 0;">+<span id="LC872" class="line" lang="cpp"> </span>
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849
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873
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<pre style="margin: 0;"> <span id="LC873" class="line" lang="cpp"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b_count</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">();</span></span>
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874
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<pre style="margin: 0;">+<span id="LC874" class="line" lang="cpp"> <span class="n" style="color: #333;">b_tbe</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Check_Button</span><span class="p">(</span><span class="n" style="color: #333;">b_yes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span><span class="p">(),</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="mi" style="color: #099;">265</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"Transfer Bootstrap Expectation method"</span><span class="p">);</span></span>
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875
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<pre style="margin: 0;">+<span id="LC875" class="line" lang="cpp"> <span class="n" style="color: #333;">b_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</span><span class="p">();</span></span>
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876
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<pre style="margin: 0;">+<span id="LC876" class="line" lang="cpp"> <span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">b_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">();</span></span>
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850
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<td class="diff-line-num new_line" data-linenumber="877" 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">
877
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<pre style="margin: 0;"> <span id="LC877" class="line" lang="cpp"> <span class="n" style="color: #333;">b_keep_trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Check_Button</span><span class="p">(</span><span class="n" style="color: #333;">b_yes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span><span class="p">(),</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="mi" style="color: #099;">180</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"Show bootstrap trees"</span><span class="p">);</span></span>
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851
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878
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<pre style="margin: 0;"> <span id="LC878" class="line" lang="cpp"> <span class="n" style="color: #333;">b_keep_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</span><span class="p">();</span></span>
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879
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<pre style="margin: 0;">+<span id="LC879" class="line" lang="cpp"></span>
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852
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880
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<pre style="margin: 0;"> <span id="LC880" class="line" lang="cpp"> <span class="n" style="color: #333;">b_alrt</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">support_cb</span><span class="p">,</span> <span class="n" style="color: #333;">b_yes</span><span class="p">);</span></span>
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853
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881
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<pre style="margin: 0;"> <span id="LC881" class="line" lang="cpp"> <span class="n" style="color: #333;">b_no</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">support_cb</span><span class="p">,</span> <span class="n" style="color: #333;">b_yes</span><span class="p">);</span></span>
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854
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<td class="diff-line-num new_line" data-linenumber="882" 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">
882
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<pre style="margin: 0;"> <span id="LC882" class="line" lang="cpp"> <span class="n" style="color: #333;">b_yes</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">support_cb</span><span class="p">,</span> <span class="n" style="color: #333;">b_yes</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1219" 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="1247" 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">@@ -1219,7 +1247,7 @@ void run_phyml_callback(Fl_Widget *ob, void *data)</td>
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<td class="diff-line-num old_line" data-linenumber="1219" 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">
1219
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<td class="diff-line-num new_line" data-linenumber="1247" 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">
1247
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<pre style="margin: 0;"> <span id="LC1247" class="line" lang="cpp"> <span class="n" style="color: #333;">fclose</span><span class="p">(</span><span class="n" style="color: #333;">in</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1220" 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">
1220
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<td class="diff-line-num new_line" data-linenumber="1248" 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">
1248
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<pre style="margin: 0;"> <span id="LC1248" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1221" 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">
1221
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<td class="diff-line-num new_line" data-linenumber="1249" 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">
1249
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<pre style="margin: 0;"> <span id="LC1249" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1222" 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">
1222
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<td class="diff-line-num new_line old" data-linenumber="1250" 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="LC1222" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">replicates</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;"><span class="idiff left">b_keep_trees</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff right">(</span>))</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1223" 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="1250" 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">
1250
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<pre style="margin: 0;">+<span id="LC1250" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">replicates</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">b_keep_trees</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff">()</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">b_tbe</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff right">()</span>))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1223" 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">
1223
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<td class="diff-line-num new_line" data-linenumber="1251" 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">
1251
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<pre style="margin: 0;"> <span id="LC1251" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s.phy_phyml_boot_trees.txt"</span><span class="p">,</span> <span class="n" style="color: #333;">base_fname</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1224" 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">
1224
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<td class="diff-line-num new_line" data-linenumber="1252" 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">
1252
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<pre style="margin: 0;"> <span id="LC1252" class="line" lang="cpp"> <span class="n" style="color: #333;">in</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fopen</span><span class="p">(</span><span class="n" style="color: #333;">input</span><span class="p">,</span> <span class="s" style="color: #d14;">"r"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1225" 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">
1225
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<td class="diff-line-num new_line" data-linenumber="1253" 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">
1253
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<pre style="margin: 0;"> <span id="LC1253" 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;">in</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1271" 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="1299" 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">@@ -1271,18 +1299,47 @@ void run_phyml_callback(Fl_Widget *ob, void *data)</td>
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1271
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<td class="diff-line-num new_line" data-linenumber="1299" 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">
1299
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<pre style="margin: 0;"> <span id="LC1299" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1272" 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">
1272
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<td class="diff-line-num new_line" data-linenumber="1300" 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">
1300
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<pre style="margin: 0;"> <span id="LC1300" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1273" 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">
1273
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<td class="diff-line-num new_line" data-linenumber="1301" 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">
1301
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<pre style="margin: 0;"> <span id="LC1301" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//clean tree internal labels</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1274" 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">
1274
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<td class="diff-line-num new_line old" data-linenumber="1302" 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="LC1274" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">replicates</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;">display_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bootstrap_reformat</span><span class="p">(</span><span class="n" style="color: #333;">display_tree</span><span class="p">,</span> <span class="n" style="color: #333;">replicates</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1275" 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="1302" 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">
1302
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<pre style="margin: 0;">+<span id="LC1302" class="line" lang="cpp"> <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;">display_tree_tbe</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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<td class="diff-line-num new old_line" data-linenumber="1275" 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="1303" 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">
1303
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<pre style="margin: 0;">+<span id="LC1303" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">replicates</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1275" 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="1304" 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">
1304
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<pre style="margin: 0;">+<span id="LC1304" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">b_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">()){</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1275" 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="1305" 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">
1305
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<pre style="margin: 0;">+<span id="LC1305" class="line" lang="cpp"> <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;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">strdup</span><span class="p">(</span><span class="n" style="color: #333;">display_tree</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1275" 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="1306" 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">
1306
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<pre style="margin: 0;">+<span id="LC1306" class="line" lang="cpp"> <span class="n" style="color: #333;">display_tree_tbe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TBE_Compute</span><span class="p">(</span><span class="n" style="color: #333;">tmp</span><span class="p">,</span> <span class="n" style="color: #333;">bootstrap_trees</span><span class="p">);</span></span>
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1307
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<pre style="margin: 0;">+<span id="LC1307" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1308" 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">
1308
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<pre style="margin: 0;">+<span id="LC1308" class="line" lang="cpp"> <span class="n" style="color: #333;">display_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bootstrap_reformat</span><span class="p">(</span><span class="n" style="color: #333;">display_tree</span><span class="p">,</span> <span class="n" style="color: #333;">replicates</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1309" 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">
1309
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<pre style="margin: 0;">+<span id="LC1309" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">bootstrap_trees</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">b_keep_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1310" 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">
1310
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<pre style="margin: 0;">+<span id="LC1310" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">bootstrap_trees</span><span class="p">);</span></span>
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1311
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<pre style="margin: 0;">+<span id="LC1311" class="line" lang="cpp"> <span class="n" style="color: #333;">bootstrap_trees</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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1312
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<pre style="margin: 0;">+<span id="LC1312" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1313" 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">
1313
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<pre style="margin: 0;">+<span id="LC1313" class="line" lang="cpp"> <span class="p">}</span></span>
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1275
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<td class="diff-line-num new_line" data-linenumber="1314" 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">
1314
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<pre style="margin: 0;"> <span id="LC1314" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">replicates</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;">display_tree</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alrt_reformat</span><span class="p">(</span><span class="n" style="color: #333;">display_tree</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1276" 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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1315
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<pre style="margin: 0;">+<span id="LC1315" class="line" lang="cpp"> </span>
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1276
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<td class="diff-line-num new_line" data-linenumber="1316" 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">
1316
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<pre style="margin: 0;"> <span id="LC1316" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//assemble tree description</span></span>
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<td class="diff-line-num old_line" data-linenumber="1277" 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">
1277
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<td class="diff-line-num new_line" data-linenumber="1317" 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">
1317
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<pre style="margin: 0;"> <span id="LC1317" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">tree_label</span><span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">];</span></span>
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<td class="diff-line-num old_line" data-linenumber="1278" 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">
1278
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<td class="diff-line-num new_line" data-linenumber="1318" 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">
1318
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<pre style="margin: 0;"> <span id="LC1318" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">,</span> <span class="s" style="color: #d14;">"PhyML ln(L)=%.1f %d sites %s"</span><span class="p">,</span> <span class="n" style="color: #333;">logL</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">modelname</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1279" 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">
1279
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<td class="diff-line-num new_line old" data-linenumber="1319" 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="LC1279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">replicates</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;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">),</span> <span class="s" style="color: #d14;">" %d replic."</span><span class="p">,</span> <span class="n" style="color: #333;">replicates</span><span class="p">);</span></span>
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1319
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<pre style="margin: 0;">+<span id="LC1319" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">replicates</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1320" 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">
1320
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<pre style="margin: 0;">+<span id="LC1320" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">),</span> <span class="s" style="color: #d14;">" %d replic."</span><span class="p">,</span> <span class="n" style="color: #333;">replicates</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1321" 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">
1321
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<pre style="margin: 0;">+<span id="LC1321" class="line" lang="cpp"> <span class="p">}</span></span>
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1280
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<td class="diff-line-num new_line" data-linenumber="1322" 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">
1322
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<pre style="margin: 0;"> <span id="LC1322" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cats</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;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">),</span> <span class="s" style="color: #d14;">" %d rate classes"</span><span class="p">,</span> <span class="n" style="color: #333;">cats</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1281" 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">
1281
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<td class="diff-line-num new_line" data-linenumber="1323" 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">
1323
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<pre style="margin: 0;"> <span id="LC1323" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">user_tree</span><span class="p">)</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">,</span> <span class="s" style="color: #d14;">" User-tree"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1282" 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">
1282
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<td class="diff-line-num new_line" data-linenumber="1324" 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">
1324
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<pre style="margin: 0;"> <span id="LC1324" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//add label to tree</span></span>
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<td class="diff-line-num old_line" data-linenumber="1283" 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">
1283
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<td class="diff-line-num new_line" data-linenumber="1325" 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">
1325
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<pre style="margin: 0;"> <span id="LC1325" class="line" lang="cpp"> <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</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">display_tree</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1284" 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">
1284
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1326
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<pre style="margin: 0;"> <span id="LC1326" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="s" style="color: #d14;">"[%s] %s"</span><span class="p">,</span> <span class="n" style="color: #333;">tree_label</span><span class="p">,</span> <span class="n" style="color: #333;">display_tree</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1285" 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">
1285
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<td class="diff-line-num new_line" data-linenumber="1327" 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">
1327
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<pre style="margin: 0;"> <span id="LC1327" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">display_tree</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1328" 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">
1328
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<pre style="margin: 0;">+<span id="LC1328" class="line" lang="cpp"> </span>
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<td class="diff-line-num new new_line" data-linenumber="1329" 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">
1329
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<pre style="margin: 0;">+<span id="LC1329" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">replicates</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">b_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1330" 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">
1330
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<pre style="margin: 0;">+<span id="LC1330" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//assemble TBE tree description</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1331" 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">
1331
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<pre style="margin: 0;">+<span id="LC1331" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">tree_label_tbe</span><span class="p">[</span><span class="mi" style="color: #099;">100</span><span class="p">];</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1332" 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">
1332
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<pre style="margin: 0;">+<span id="LC1332" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label_tbe</span><span class="p">,</span> <span class="s" style="color: #d14;">"PhyML ln(L)=%.1f %d sites %s"</span><span class="p">,</span> <span class="n" style="color: #333;">logL</span><span class="p">,</span> <span class="n" style="color: #333;">seqlen</span><span class="p">,</span> <span class="n" style="color: #333;">modelname</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1333" 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">
1333
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<pre style="margin: 0;">+<span id="LC1333" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label_tbe</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label_tbe</span><span class="p">),</span> <span class="s" style="color: #d14;">" %d replic. (TBE)"</span><span class="p">,</span> <span class="n" style="color: #333;">replicates</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1334" 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">
1334
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<pre style="margin: 0;">+<span id="LC1334" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">cats</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;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree_label_tbe</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label_tbe</span><span class="p">),</span> <span class="s" style="color: #d14;">" %d rate classes"</span><span class="p">,</span> <span class="n" style="color: #333;">cats</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1335" 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">
1335
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<pre style="margin: 0;">+<span id="LC1335" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">user_tree</span><span class="p">)</span> <span class="n" style="color: #333;">strcat</span><span class="p">(</span><span class="n" style="color: #333;">tree_label_tbe</span><span class="p">,</span> <span class="s" style="color: #d14;">" User-tree"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1336" 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">
1336
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<pre style="margin: 0;">+<span id="LC1336" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//add label to tree</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1337" 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">
1337
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<pre style="margin: 0;">+<span id="LC1337" class="line" lang="cpp"> <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</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">tree_label_tbe</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">display_tree_tbe</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1338" 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">
1338
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<pre style="margin: 0;">+<span id="LC1338" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="s" style="color: #d14;">"[%s] %s"</span><span class="p">,</span> <span class="n" style="color: #333;">tree_label_tbe</span><span class="p">,</span> <span class="n" style="color: #333;">display_tree_tbe</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1339" 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">
1339
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<pre style="margin: 0;">+<span id="LC1339" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">display_tree_tbe</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1340" 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">
1340
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<pre style="margin: 0;">+<span id="LC1340" class="line" lang="cpp"> <span class="n" style="color: #333;">display_tree_tbe</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tree</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1341" 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">
1341
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<pre style="margin: 0;">+<span id="LC1341" class="line" lang="cpp"> <span class="p">}</span></span>
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1342
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<pre style="margin: 0;">+<span id="LC1342" class="line" lang="cpp"> </span>
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1286
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<td class="diff-line-num new_line" data-linenumber="1343" 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">
1343
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<pre style="margin: 0;"> <span id="LC1343" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_view_valid</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1287" 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">
1287
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<td class="diff-line-num new_line" data-linenumber="1344" 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">
1344
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<pre style="margin: 0;"> <span id="LC1344" 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;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">extract_filename</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">masename</span><span class="p">);</span></span>
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1288
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1345
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<pre style="margin: 0;"> <span id="LC1345" class="line" lang="cpp"> <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;">title</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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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1293" 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">@@ -1293,13 +1350,19 @@ void run_phyml_callback(Fl_Widget *ob, void *data)</td>
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1293
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1350
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<pre style="margin: 0;"> <span id="LC1350" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s-%s"</span><span class="p">,</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="s" style="color: #d14;">"PhyML_tree"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1294" 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">
1294
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1351
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<pre style="margin: 0;"> <span id="LC1351" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'.'</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1295" 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">
1295
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1352
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<pre style="margin: 0;"> <span id="LC1352" class="line" lang="cpp"> <span class="p">}</span></span>
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1296
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<td class="diff-line-num new_line old" data-linenumber="1353" 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="LC1296" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Window</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">btreew</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">treew</span></span><span class="p">;</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1297" 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">
1297
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<td class="diff-line-num new_line old" data-linenumber="1353" 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="LC1297" 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">bootstrap_trees</span></span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1298" 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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1353
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<pre style="margin: 0;">+<span id="LC1353" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Window</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">btreew</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">treew</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">;</span></span>
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1354
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<pre style="margin: 0;">+<span id="LC1354" 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">replicates</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</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">b_keep_trees</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">value</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="1298" 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">
1298
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<td class="diff-line-num new_line" data-linenumber="1355" 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">
1355
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<pre style="margin: 0;"> <span id="LC1355" class="line" lang="cpp"> <span class="n" style="color: #333;">btreew</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">treedraw</span><span class="p">(</span><span class="n" style="color: #333;">bootstrap_trees</span><span class="p">,</span> <span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="s" style="color: #d14;">"bootstrap trees"</span><span class="p">,</span> <span class="n" style="color: #333;">FALSE</span><span class="p">);</span></span>
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1299
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1356
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<pre style="margin: 0;"> <span id="LC1356" class="line" lang="cpp"> <span class="p">}</span></span>
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1357
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<pre style="margin: 0;">+<span id="LC1357" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">replicates</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">b_tbe</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">value</span><span class="p">())</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1358" 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">
1358
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<pre style="margin: 0;">+<span id="LC1358" 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;">p</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"PhyML_tree"</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1359" 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">
1359
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<pre style="margin: 0;">+<span id="LC1359" class="line" lang="cpp"> <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;">q</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span><span class="p">)</span><span class="n" style="color: #333;">malloc</span><span class="p">(</span><span class="n" style="color: #333;">strlen</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1360" 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">
1360
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<pre style="margin: 0;">+<span id="LC1360" class="line" lang="cpp"> <span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="s" style="color: #d14;">"%s_TBE"</span><span class="p">,</span> <span class="n" style="color: #333;">p</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1361" 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">
1361
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<pre style="margin: 0;">+<span id="LC1361" class="line" lang="cpp"> <span class="n" style="color: #333;">treedraw</span><span class="p">(</span><span class="n" style="color: #333;">display_tree_tbe</span><span class="p">,</span> <span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">q</span><span class="p">,</span> <span class="n" style="color: #333;">FALSE</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1362" 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">
1362
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<pre style="margin: 0;">+<span id="LC1362" class="line" lang="cpp"> <span class="p">}</span></span>
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1300
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<td class="diff-line-num new_line" data-linenumber="1363" 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">
1363
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<pre style="margin: 0;"> <span id="LC1363" class="line" lang="cpp"> <span class="n" style="color: #333;">treew</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">treedraw</span><span class="p">(</span><span class="n" style="color: #333;">tree</span><span class="p">,</span> <span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">title</span><span class="o" style="font-weight: 600;">:</span><span class="s" style="color: #d14;">"PhyML_tree"</span><span class="p">,</span> <span class="n" style="color: #333;">FALSE</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="1301" 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">
1301
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<td class="diff-line-num new_line" data-linenumber="1364" 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">
1364
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<pre style="margin: 0;"> <span id="LC1364" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#if !defined(__APPLE__)</span></span>
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1302
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<pre style="margin: 0;">-<span id="LC1302" 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">bootstrap_trees</span></span><span class="p">)</span> <span class="n" style="color: #333;">treew</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">(</span><span class="n" style="color: #333;">btreew</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="n" style="color: #333;">btreew</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">40</span><span class="p">);</span></span>
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1365
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<pre style="margin: 0;">+<span id="LC1365" 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">treew</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">btreew</span></span><span class="p">)</span> <span class="n" style="color: #333;">treew</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">position</span><span class="p">(</span><span class="n" style="color: #333;">btreew</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">30</span><span class="p">,</span> <span class="n" style="color: #333;">btreew</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">40</span><span class="p">);</span></span>
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1303
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<td class="diff-line-num new_line" data-linenumber="1366" 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">
1366
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<pre style="margin: 0;"> <span id="LC1366" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif</span></span>
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1304
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<td class="diff-line-num new_line" data-linenumber="1367" 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">
1367
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<pre style="margin: 0;"> <span id="LC1367" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">delete</span><span class="p">[]</span> <span class="n" style="color: #333;">title</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="1305" 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">
1305
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<td class="diff-line-num new_line" data-linenumber="1368" 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">
1368
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<pre style="margin: 0;"> <span id="LC1368" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2133" 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="2196" 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">@@ -2133,7 +2196,8 @@ void parsimony_dialog(SEA_VIEW *view)</td>
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2133
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<td class="diff-line-num new_line" data-linenumber="2196" 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">
2196
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<pre style="margin: 0;"> <span id="LC2196" class="line" lang="cpp"> <span class="n" style="color: #333;">w_btrepl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">align</span><span class="p">(</span><span class="n" style="color: #333;">FL_ALIGN_RIGHT</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2134" 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">
2134
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<td class="diff-line-num new_line" data-linenumber="2197" 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">
2197
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<pre style="margin: 0;"> <span id="LC2197" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Check_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">keep_b_trees</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Check_Button</span><span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span> <span class="n" style="color: #333;">w_dobootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">w_dobootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="mi" style="color: #099;">180</span><span class="p">,</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="s" style="color: #d14;">"Show bootstrap trees"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2135" 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">
2135
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<td class="diff-line-num new_line" data-linenumber="2198" 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">
2198
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<pre style="margin: 0;"> <span id="LC2198" class="line" lang="cpp"> <span class="n" style="color: #333;">keep_b_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">deactivate</span><span class="p">();</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2136" 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">
2136
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<td class="diff-line-num new_line old" data-linenumber="2199" 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="LC2136" class="line" lang="cpp"> <span class="n" style="color: #333;">w_dobootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">dist_b_cb</span><span class="p">,</span> <span class="n" style="color: #333;">keep_b_trees</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2137" 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="2199" 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">
2199
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<pre style="margin: 0;">+<span id="LC2199" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">Fl_Check_Button</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">buttons</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="n" style="color: #333;">keep_b_trees</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">};</span></span>
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2200
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<pre style="margin: 0;">+<span id="LC2200" class="line" lang="cpp"> <span class="n" style="color: #333;">w_dobootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">callback</span><span class="p">(</span><span class="n" style="color: #333;">dist_b_cb</span><span class="p">,</span> <span class="n" style="color: #333;">buttons</span><span class="p">);</span></span>
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2137
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<td class="diff-line-num new_line" data-linenumber="2201" 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">
2201
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<pre style="margin: 0;"> <span id="LC2201" class="line" lang="cpp"> <span class="n" style="color: #333;">w_dobootstrap</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">when</span><span class="p">(</span><span class="n" style="color: #333;">FL_WHEN_CHANGED</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2138" 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">
2138
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<td class="diff-line-num new_line" data-linenumber="2202" 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">
2202
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<pre style="margin: 0;"> <span id="LC2202" class="line" lang="cpp"></span>
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<td class="diff-line-num old_line" data-linenumber="2139" 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">
2139
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<td class="diff-line-num new_line" data-linenumber="2203" 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">
2203
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<pre style="margin: 0;"> <span id="LC2203" class="line" lang="cpp"> <span class="n" style="color: #333;">Fl_Box</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">w_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">Fl_Box</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="n" style="color: #333;">keep_b_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">keep_b_trees</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">h</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">w</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">w</span><span class="p">(),</span> <span class="mi" style="color: #099;">20</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2744" 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="2808" 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">@@ -2744,7 +2808,7 @@ void command_line_phylogeny(int argc, char **argv)</td>
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2744
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2808
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<pre style="margin: 0;"> <span id="LC2808" class="line" lang="cpp"> </span>
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2745
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<td class="diff-line-num new_line" data-linenumber="2809" 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">
2809
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<pre style="margin: 0;"> <span id="LC2809" class="line" lang="cpp"> <span class="n" style="color: #333;">view</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">tot_trees</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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2746
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<td class="diff-line-num new_line" data-linenumber="2810" 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">
2810
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<pre style="margin: 0;"> <span id="LC2810" 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;">run_distance_method</span><span class="p">(</span><span class="n" style="color: #333;">view</span><span class="p">,</span> <span class="n" style="color: #333;">distkind</span><span class="p">,</span> <span class="n" style="color: #333;">isarg</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"-nogaps"</span><span class="p">),</span> <span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">isarg</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"-NJ"</span><span class="p">),</span> <span class="n" style="color: #333;">replicates</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;">replicates</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2747" 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">
2747
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<td class="diff-line-num new_line old" data-linenumber="2811" 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="LC2747" class="line" lang="cpp"> <span class="n" style="color: #333;">distname</span><span class="p">,</span> <span class="n" style="color: #333;">distkind</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Ka</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">distkind</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Ks</span><span class="p">,</span> <span class="n" style="color: #333;">argname</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"-distance_matrix"</span><span class="p">),</span> <span class="n" style="color: #333;">utree</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">Fl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fatal</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2748" 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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2811
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<pre style="margin: 0;">+<span id="LC2811" class="line" lang="cpp"> <span class="n" style="color: #333;">distname</span><span class="p">,</span> <span class="n" style="color: #333;">distkind</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Ka</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">distkind</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">Ks</span><span class="p">,</span> <span class="n" style="color: #333;">argname</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"-distance_matrix"</span><span class="p">),</span> <span class="n" style="color: #333;">utree</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="n" style="color: #333;">Fl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fatal</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2748" 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">
2748
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<td class="diff-line-num new_line" data-linenumber="2812" 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">
2812
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<pre style="margin: 0;"> <span id="LC2812" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isarg</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">,</span> <span class="s" style="color: #d14;">"-distance_matrix"</span><span class="p">))</span> <span class="n" style="color: #333;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="2749" 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">
2749
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<td class="diff-line-num new_line" data-linenumber="2813" 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">
2813
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<pre style="margin: 0;"> <span id="LC2813" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="2750" 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">
2750
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<td class="diff-line-num new_line" data-linenumber="2814" 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">
2814
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<pre style="margin: 0;"> <span id="LC2814" class="line" lang="cpp"> </span>
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