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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/gubbins">Debian Med / gubbins</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/gubbins/commit/490cb88e0c973df3eb02e7e7b3d8e71ee1a80f75">490cb88e</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-12-20T23:00:10Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.5</pre>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<span class="new-file">
+
CHANGELOG.md
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<li class="file-stats">
<a href="#6651ddff6eb82c840ced7c1dddee15c6e1913dd4">
Dockerfile
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<li class="file-stats">
<a href="#b2270542d41297db1ee0d12698e609ea3ec25ce7">
<span class="deleted-file">
−
INSTALL.md
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<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#2be6fe092a42753d652cbb209e2d5f96d7c5e1ef">
CHANGELOG
→
obsolete_changelog
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</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/gubbins/commit/490cb88e0c973df3eb02e7e7b3d8e71ee1a80f75#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="15" 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">@@ -15,10 +15,15 @@ cache:</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">build"</span></span>
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<td class="diff-line-num old_line" data-linenumber="16" 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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">$HOME/.cache/pip"</span></span>
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<td class="diff-line-num old_line" data-linenumber="17" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>
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<td class="diff-line-num new_line old" data-linenumber="18" 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="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.<span class="idiff left right">4</span>"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(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="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.<span class="idiff left right">5</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">source</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">./install_dependencies.sh"</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">autoreconf</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">-i"</span></span>
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<td class="diff-line-num old old_line" data-linenumber="23" 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="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">./configure"</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">make</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">check"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"><span class="na" style="color: #008080;">before_script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install codecov</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">autoreconf -i && ./configure --enable-maintainer-mode CFLAGS='-O0 --coverage' && make && make check</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cd python && coverage run setup.py test</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"><span class="na" style="color: #008080;">after_success</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">bash <(curl -s https://codecov.io/bash)</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">codecov</span></span></pre>
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<a href="https://salsa.debian.org/med-team/gubbins/commit/490cb88e0c973df3eb02e7e7b3d8e71ee1a80f75#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Change Log</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [Unreleased](https://github.com/sanger-pathogens/gubbins/tree/HEAD)</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.3.4...HEAD</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Implemented enhancements:**</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(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="LC9" class="line" lang="markdown"><span class="p">-</span> Retaining recombinant free non-polymorphic sites <span class="p">[</span><span class="nv" style="color: #008080;">\#208</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/208</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">-</span> Segmentation fault with some input files <span class="p">[</span><span class="nv" style="color: #008080;">\#170</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/170</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">-</span> ltmain.sh should be removed? <span class="p">[</span><span class="nv" style="color: #008080;">\#157</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/157</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p">-</span> Gubbins not generating final<span class="se" style="color: #d14;">\_</span>tree.tre <span class="p">[</span><span class="nv" style="color: #008080;">\#253</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/253</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(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="LC19" class="line" lang="markdown"><span class="p">-</span> Can gubbins take the fasta file produced by snp-sites as inputs? <span class="p">[</span><span class="nv" style="color: #008080;">\#250</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/250</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p">-</span> rho/theta--<span class="se" style="color: #d14;">\></span> total recombination events? <span class="p">[</span><span class="nv" style="color: #008080;">\#247</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/247</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">-</span> Gubbins output: internal<span class="se" style="color: #d14;">\_</span>5 / internal<span class="se" style="color: #d14;">\_</span>6 node? <span class="p">[</span><span class="nv" style="color: #008080;">\#246</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/246</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">-</span> recombination<span class="se" style="color: #d14;">\_</span>predictions.gff regions are overlapping and duplicated ? <span class="p">[</span><span class="nv" style="color: #008080;">\#240</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/240</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(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="LC23" class="line" lang="markdown"><span class="p">-</span> Gubbins crashed, please ensure you have enough free memory <span class="p">[</span><span class="nv" style="color: #008080;">\#239</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/239</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p">-</span> GFF file output columns <span class="p">[</span><span class="nv" style="color: #008080;">\#234</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/234</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">-</span> what does "Bases in Recombinations" in the stats file refer to? <span class="p">[</span><span class="nv" style="color: #008080;">\#232</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/232</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p">-</span> Make the FTP urls actual hyperlinks <span class="p">[</span><span class="nv" style="color: #008080;">\#229</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/229</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p">-</span> Failing test on 2.1.0 <span class="p">[</span><span class="nv" style="color: #008080;">\#177</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/177</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p">-</span> Rename exec in docker <span class="p">[</span><span class="nv" style="color: #008080;">\#260</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/260</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p">-</span> Mark as unmaintained <span class="p">[</span><span class="nv" style="color: #008080;">\#259</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/259</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p">-</span> 627258 codecov <span class="p">[</span><span class="nv" style="color: #008080;">\#244</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/244</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p">-</span> Add changelog <span class="p">[</span><span class="nv" style="color: #008080;">\#242</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/242</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p">-</span> Rt574328 readme <span class="p">[</span><span class="nv" style="color: #008080;">\#241</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/241</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p">-</span> Remove INSTALL file <span class="p">[</span><span class="nv" style="color: #008080;">\#238</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/238</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"><span class="p">-</span> 574328 edit readme <span class="p">[</span><span class="nv" style="color: #008080;">\#237</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/237</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="p">-</span> update changelog <span class="p">[</span><span class="nv" style="color: #008080;">\#228</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/228</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.3.4](https://github.com/sanger-pathogens/gubbins/tree/v2.3.4) (2018-07-30)</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.3.3...v2.3.4</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p">-</span> dynamically allocate memory to avoid stack overflow <span class="p">[</span><span class="nv" style="color: #008080;">\#227</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/227</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.3.3](https://github.com/sanger-pathogens/gubbins/tree/v2.3.3) (2018-07-26)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.3.2...v2.3.3</span><span class="p">)</span></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p">-</span> ' INSTALL' doesn't link to INSTALL.md <span class="p">[</span><span class="nv" style="color: #008080;">\#222</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/222</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown"><span class="p">-</span> Dockerfile independent from debian package <span class="p">[</span><span class="nv" style="color: #008080;">\#226</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/226</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown"><span class="p">-</span> universal link <span class="p">[</span><span class="nv" style="color: #008080;">\#224</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/224</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="p">-</span> link to install.md <span class="p">[</span><span class="nv" style="color: #008080;">\#223</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/223</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
</pre>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown"></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">
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.3.2](https://github.com/sanger-pathogens/gubbins/tree/v2.3.2) (2018-06-15)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.3.1...v2.3.2</span><span class="p">)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"></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">
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Implemented enhancements:**</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"><span class="p">-</span> Direct output to a directory <span class="p">[</span><span class="nv" style="color: #008080;">\#209</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/209</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"></span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown"><span class="p">-</span> Warning while parsing tree: non-numeric label N38 for internal node <span class="p">[</span><span class="nv" style="color: #008080;">\#154</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/154</span><span class="p">)</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown"><span class="p">-</span> Is there minimum sample size to use gubbins? <span class="p">[</span><span class="nv" style="color: #008080;">\#213</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/213</span><span class="p">)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"><span class="p">-</span> gubbins<span class="se" style="color: #d14;">\_</span>drawer graph <span class="p">[</span><span class="nv" style="color: #008080;">\#212</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/212</span><span class="p">)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"><span class="p">-</span> Running example files <span class="p">[</span><span class="nv" style="color: #008080;">\#211</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/211</span><span class="p">)</span></span>
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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="markdown"><span class="p">-</span> TypeError: reroot<span class="se" style="color: #d14;">\_</span>at<span class="se" style="color: #d14;">\_</span>midpoint<span class="se" style="color: #d14;">\(\)</span> got an unexpected keyword argument 'update<span class="se" style="color: #d14;">\_</span>splits' <span class="p">[</span><span class="nv" style="color: #008080;">\#205</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/205</span><span class="p">)</span></span>
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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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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown"><span class="p">-</span> x <span class="p">[</span><span class="nv" style="color: #008080;">\#204</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/204</span><span class="p">)</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="p">-</span> Input format is not clear <span class="p">[</span><span class="nv" style="color: #008080;">\#185</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/185</span><span class="p">)</span></span>
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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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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown"><span class="p">-</span> Inconsistencies in branch stats file <span class="p">[</span><span class="nv" style="color: #008080;">\#181</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/181</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"><span class="p">-</span> error while loading shared libraries: libgubbins.so.0 <span class="p">[</span><span class="nv" style="color: #008080;">\#156</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/156</span><span class="p">)</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown"></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="markdown"><span class="p">-</span> Replaced the script gubbins<span class="se" style="color: #d14;">\_</span>drawer.py with an empty script displaying… <span class="p">[</span><span class="nv" style="color: #008080;">\#221</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/221</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</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="markdown"><span class="p">-</span> Link check to lsubunit <span class="p">[</span><span class="nv" style="color: #008080;">\#220</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/220</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
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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
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"><span class="p">-</span> corrected typo: 'fastree' -<span class="se" style="color: #d14;">\></span> 'fasttree' <span class="p">[</span><span class="nv" style="color: #008080;">\#219</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/219</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[puethe](https://github.com/puethe</span><span class="p">)</span>)</span>
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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
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown"><span class="p">-</span> update instructions for Docker <span class="p">[</span><span class="nv" style="color: #008080;">\#217</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/217</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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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
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="p">-</span> added choices to <span class="sb" style="color: #d14;">`--tree\_builder`</span> and other args <span class="p">[</span><span class="nv" style="color: #008080;">\#207</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/207</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[schultzm](https://github.com/schultzm</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown"><span class="p">-</span> ignore ltmain.sh for language statistics <span class="p">[</span><span class="nv" style="color: #008080;">\#206</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/206</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"><span class="p">-</span> update manual <span class="p">[</span><span class="nv" style="color: #008080;">\#203</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/203</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.3.1](https://github.com/sanger-pathogens/gubbins/tree/v2.3.1) (2017-09-22)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.3.0...v2.3.1</span><span class="p">)</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown"><span class="p">-</span> gubbins<span class="se" style="color: #d14;">\_</span>drawer.py help improvement <span class="p">[</span><span class="nv" style="color: #008080;">\#183</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/183</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="markdown"></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"><span class="p">-</span> Internal nodes <span class="p">[</span><span class="nv" style="color: #008080;">\#202</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/202</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="103" style="width: 35px; color: rgba(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="LC103" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.3.0](https://github.com/sanger-pathogens/gubbins/tree/v2.3.0) (2017-09-21)</span></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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.2.3...v2.3.0</span><span class="p">)</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"><span class="p">-</span> Some options have default listed twice in --help <span class="p">[</span><span class="nv" style="color: #008080;">\#199</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/199</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="112" style="width: 35px; color: rgba(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="LC112" class="line" lang="markdown"><span class="p">-</span> Gubbins drawer help text <span class="p">[</span><span class="nv" style="color: #008080;">\#201</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/201</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.3](https://github.com/sanger-pathogens/gubbins/tree/v2.2.3) (2017-09-15)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.2.2...v2.2.3</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="markdown"></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">
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="markdown"></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="markdown"><span class="p">-</span> Error running gubbins<span class="se" style="color: #d14;">\_</span>drawer.py with v. 2.2.0 <span class="p">[</span><span class="nv" style="color: #008080;">\#184</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/184</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="markdown"></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="markdown"><span class="p">-</span> Support raxml-AVX2 if available <span class="p">[</span><span class="nv" style="color: #008080;">\#196</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/196</span><span class="p">)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="markdown"><span class="p">-</span> brew install gubbins errors - no formula for pillow <span class="p">[</span><span class="nv" style="color: #008080;">\#194</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/194</span><span class="p">)</span></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">
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="markdown"><span class="p">-</span> gubbins would not run <span class="p">[</span><span class="nv" style="color: #008080;">\#187</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/187</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="129" style="width: 35px; color: rgba(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="LC129" class="line" lang="markdown"><span class="p">-</span> Fix default extended help text. <span class="p">[</span><span class="nv" style="color: #008080;">\#200</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/200</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="p">-</span> allow for AVX2 <span class="p">[</span><span class="nv" style="color: #008080;">\#197</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/197</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"></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">
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.2](https://github.com/sanger-pathogens/gubbins/tree/v2.2.2) (2017-09-04)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.2.1...v2.2.2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="markdown"></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="markdown"><span class="p">-</span> Forgot to make a 2.2.1 release? <span class="p">[</span><span class="nv" style="color: #008080;">\#195</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/195</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="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.1](https://github.com/sanger-pathogens/gubbins/tree/v2.2.1) (2017-08-02)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.10...v2.2.1</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="markdown"></span>
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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="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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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="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="markdown"><span class="p">-</span> Gubbins - Ns in output alignment <span class="p">[</span><span class="nv" style="color: #008080;">\#192</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/192</span><span class="p">)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="markdown"><span class="p">-</span> from gubbins import common ImportError: cannot import name common <span class="p">[</span><span class="nv" style="color: #008080;">\#191</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/191</span><span class="p">)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="markdown"><span class="p">-</span> Losing taxa? <span class="p">[</span><span class="nv" style="color: #008080;">\#189</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/189</span><span class="p">)</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="markdown"></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">
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="markdown"><span class="p">-</span> updated manual <span class="p">[</span><span class="nv" style="color: #008080;">\#193</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/193</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</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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<pre style="margin: 0;">+<span id="LC151" class="line" lang="markdown"><span class="p">-</span> Manual in docx format <span class="p">[</span><span class="nv" style="color: #008080;">\#188</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/188</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</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
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="markdown"><span class="p">-</span> Fixed biopython sub<span class="se" style="color: #d14;">\_</span>features bug <span class="p">[</span><span class="nv" style="color: #008080;">\#186</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/186</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[ssjunnebo](https://github.com/ssjunnebo</span><span class="p">)</span>)</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.10](https://github.com/sanger-pathogens/gubbins/tree/v1.4.10) (2016-10-31)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.2.0...v1.4.10</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="markdown"></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="markdown"><span class="p">-</span> removing identical isolates <span class="p">[</span><span class="nv" style="color: #008080;">\#179</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/179</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="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.2.0](https://github.com/sanger-pathogens/gubbins/tree/v2.2.0) (2016-10-31)</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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.1.0...v2.2.0</span><span class="p">)</span></span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="markdown"></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</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="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="markdown"><span class="p">-</span> Linuxbrew installs 1.4.7 still <span class="p">[</span><span class="nv" style="color: #008080;">\#176</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/176</span><span class="p">)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="markdown"><span class="p">-</span> Can't find RAxML in path <span class="p">[</span><span class="nv" style="color: #008080;">\#174</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/174</span><span class="p">)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="markdown"><span class="p">-</span> Source install doesn't install python wrappers <span class="p">[</span><span class="nv" style="color: #008080;">\#173</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/173</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="markdown"></span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="markdown"></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="markdown"><span class="p">-</span> dont filter out identical sequences by default <span class="p">[</span><span class="nv" style="color: #008080;">\#180</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/180</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"></span>
</pre>
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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.1.0](https://github.com/sanger-pathogens/gubbins/tree/v2.1.0) (2016-07-22)</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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v2.0.0...v2.1.0</span><span class="p">)</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"></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="markdown"><span class="gs" style="font-weight: 600;">**Fixed bugs:**</span></span>
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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
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown"></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
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="markdown"><span class="p">-</span> slow fastml <span class="p">[</span><span class="nv" style="color: #008080;">\#167</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/167</span><span class="p">)</span></span>
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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="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="markdown"><span class="p">-</span> Use GTRCAT by default with RAxML <span class="p">[</span><span class="nv" style="color: #008080;">\#175</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/175</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="markdown"></span>
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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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<pre style="margin: 0;">+<span id="LC185" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v2.0.0](https://github.com/sanger-pathogens/gubbins/tree/v2.0.0) (2016-07-15)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.9...v2.0.0</span><span class="p">)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="markdown"></span>
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<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
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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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="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="markdown"><span class="p">-</span> .embl output file not opening in Artemis <span class="p">[</span><span class="nv" style="color: #008080;">\#165</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/165</span><span class="p">)</span></span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="markdown"></span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="markdown"><span class="p">-</span> Raxml reconstruction <span class="p">[</span><span class="nv" style="color: #008080;">\#172</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/172</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="markdown"><span class="p">-</span> Raxml reconstruction <span class="p">[</span><span class="nv" style="color: #008080;">\#171</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/171</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="markdown"></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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.9](https://github.com/sanger-pathogens/gubbins/tree/v1.4.9) (2016-04-15)</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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.8...v1.4.9</span><span class="p">)</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
</pre>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="markdown"><span class="p">-</span> Duplicate sequences <span class="p">[</span><span class="nv" style="color: #008080;">\#166</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/166</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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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<pre style="margin: 0;">+<span id="LC203" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.8](https://github.com/sanger-pathogens/gubbins/tree/v1.4.8) (2016-04-13)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.7...v1.4.8</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="markdown"></span>
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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="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="markdown"><span class="p">-</span> numpy issues <span class="p">[</span><span class="nv" style="color: #008080;">\#159</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/159</span><span class="p">)</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="markdown"><span class="p">-</span> Convert the proc output from bytes to strings <span class="p">[</span><span class="nv" style="color: #008080;">\#164</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/164</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[aaronk](https://github.com/aaronk</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.7](https://github.com/sanger-pathogens/gubbins/tree/v1.4.7) (2016-02-29)</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">
216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.6...v1.4.7</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="markdown"></span>
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<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">
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="markdown"><span class="p">-</span> midpoint rerooting by default <span class="p">[</span><span class="nv" style="color: #008080;">\#163</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/163</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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">
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="markdown"><span class="p">-</span> Fix allocation from stack bug. <span class="p">[</span><span class="nv" style="color: #008080;">\#161</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/161</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[jeromekelleher](https://github.com/jeromekelleher</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="223" style="width: 35px; color: rgba(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="LC223" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.6](https://github.com/sanger-pathogens/gubbins/tree/v1.4.6) (2016-02-29)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.5...v1.4.6</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="226" style="width: 35px; color: rgba(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="LC226" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.5](https://github.com/sanger-pathogens/gubbins/tree/v1.4.5) (2016-01-13)</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v.1.4.5...v1.4.5</span><span class="p">)</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="markdown"></span>
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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v.1.4.5](https://github.com/sanger-pathogens/gubbins/tree/v.1.4.5) (2016-01-13)</span></span>
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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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.4...v.1.4.5</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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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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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown"></span>
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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="markdown"><span class="p">-</span> remove install-sh <span class="p">[</span><span class="nv" style="color: #008080;">\#160</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/160</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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="markdown"><span class="p">-</span> Debian bug 807150 <span class="p">[</span><span class="nv" style="color: #008080;">\#158</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/158</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.4](https://github.com/sanger-pathogens/gubbins/tree/v1.4.4) (2015-12-09)</span></span>
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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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<pre style="margin: 0;">+<span id="LC238" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.3...v1.4.4</span><span class="p">)</span></span>
</pre>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.3](https://github.com/sanger-pathogens/gubbins/tree/v1.4.3) (2015-11-19)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.2...v1.4.3</span><span class="p">)</span></span>
</pre>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="markdown"></span>
</pre>
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<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">
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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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="markdown"></span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="markdown"><span class="p">-</span> multithreading <span class="p">[</span><span class="nv" style="color: #008080;">\#151</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/151</span><span class="p">)</span></span>
</pre>
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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="markdown"></span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.2](https://github.com/sanger-pathogens/gubbins/tree/v1.4.2) (2015-09-02)</span></span>
</pre>
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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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<pre style="margin: 0;">+<span id="LC248" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.1...v1.4.2</span><span class="p">)</span></span>
</pre>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="markdown"><span class="p">-</span> check for input files which are too long <span class="p">[</span><span class="nv" style="color: #008080;">\#153</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/153</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="markdown"><span class="p">-</span> update install docs <span class="p">[</span><span class="nv" style="color: #008080;">\#150</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/150</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="255" style="width: 35px; color: rgba(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="LC255" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.1](https://github.com/sanger-pathogens/gubbins/tree/v1.4.1) (2015-07-07)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.4.0...v1.4.1</span><span class="p">)</span></span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.4.0](https://github.com/sanger-pathogens/gubbins/tree/v1.4.0) (2015-07-01)</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="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.3.4...v1.4.0</span><span class="p">)</span></span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="markdown"><span class="p">-</span> "Binary package - For 64 bit Linux" links to nowhere <span class="p">[</span><span class="nv" style="color: #008080;">\#142</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/142</span><span class="p">)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="markdown"><span class="p">-</span> INSTALL file not obvious <span class="p">[</span><span class="nv" style="color: #008080;">\#129</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/129</span><span class="p">)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="markdown"><span class="p">-</span> segmentation fault <span class="p">[</span><span class="nv" style="color: #008080;">\#49</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/49</span><span class="p">)</span></span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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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="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="markdown"><span class="p">-</span> Convert python to 3 <span class="p">[</span><span class="nv" style="color: #008080;">\#149</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/149</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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">
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="markdown"><span class="p">-</span> update raxml version for travis <span class="p">[</span><span class="nv" style="color: #008080;">\#148</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/148</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</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="markdown"><span class="p">-</span> Add build status to README <span class="p">[</span><span class="nv" style="color: #008080;">\#147</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/147</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[bewt85](https://github.com/bewt85</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="markdown"><span class="p">-</span> Add TravisCI support <span class="p">[</span><span class="nv" style="color: #008080;">\#146</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/146</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[bewt85](https://github.com/bewt85</span><span class="p">)</span>)</span>
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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">
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="markdown"><span class="p">-</span> Reference URL updated to final published version not early access <span class="p">[</span><span class="nv" style="color: #008080;">\#145</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/145</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[aslett1](https://github.com/aslett1</span><span class="p">)</span>)</span>
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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">
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="markdown"><span class="p">-</span> Manually merge Aidan Delaneys pull request <span class="p">[</span><span class="nv" style="color: #008080;">\#144</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/144</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="markdown"><span class="p">-</span> Detect blocks at end of sequence <span class="p">[</span><span class="nv" style="color: #008080;">\#143</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/143</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.3.4](https://github.com/sanger-pathogens/gubbins/tree/v1.3.4) (2015-05-18)</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">
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.3.3...v1.3.4</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="markdown"></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Closed issues:**</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="markdown"><span class="p">-</span> No ./configure in github - need to run autoconf? <span class="p">[</span><span class="nv" style="color: #008080;">\#130</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues/130</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.3.3](https://github.com/sanger-pathogens/gubbins/tree/v1.3.3) (2015-04-16)</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">
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.3.1...v1.3.3</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="markdown"></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">
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="markdown"><span class="p">-</span> Window size self error <span class="p">[</span><span class="nv" style="color: #008080;">\#140</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/140</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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">
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="markdown"><span class="p">-</span> Window size self error <span class="p">[</span><span class="nv" style="color: #008080;">\#139</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/139</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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">
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="markdown"></span>
</pre>
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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">
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.3.1](https://github.com/sanger-pathogens/gubbins/tree/v1.3.1) (2015-04-16)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.3.0...v1.3.1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="markdown"></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="markdown"></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">
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="markdown"><span class="p">-</span> version 1.3.1 <span class="p">[</span><span class="nv" style="color: #008080;">\#138</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/138</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</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="markdown"></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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.3.0](https://github.com/sanger-pathogens/gubbins/tree/v1.3.0) (2015-04-16)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.2.4...v1.3.0</span><span class="p">)</span></span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="markdown"></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="markdown"></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="markdown"><span class="p">-</span> Recalculate genome length <span class="p">[</span><span class="nv" style="color: #008080;">\#137</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/137</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<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
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="markdown"><span class="p">-</span> Downstream recombinations <span class="p">[</span><span class="nv" style="color: #008080;">\#136</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/136</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.2.4](https://github.com/sanger-pathogens/gubbins/tree/v1.2.4) (2015-03-31)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.2.3...v1.2.4</span><span class="p">)</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="markdown"></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="markdown"></span>
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<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
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="markdown"><span class="p">-</span> output version in python script <span class="p">[</span><span class="nv" style="color: #008080;">\#135</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/135</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</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="markdown"></span>
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<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
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.2.3](https://github.com/sanger-pathogens/gubbins/tree/v1.2.3) (2015-03-30)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="315" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.2.2...v1.2.3</span><span class="p">)</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="markdown"><span class="p">-</span> include last element of array <span class="p">[</span><span class="nv" style="color: #008080;">\#134</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/134</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.2.2](https://github.com/sanger-pathogens/gubbins/tree/v1.2.2) (2015-03-30)</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.2.1...v1.2.2</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="markdown"></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.2.1](https://github.com/sanger-pathogens/gubbins/tree/v1.2.1) (2015-03-30)</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.2.0...v1.2.1</span><span class="p">)</span></span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="markdown"><span class="p">-</span> Correct vcf format and EMBL format <span class="p">[</span><span class="nv" style="color: #008080;">\#133</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/133</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="markdown"><span class="p">-</span> debian changelog <span class="p">[</span><span class="nv" style="color: #008080;">\#132</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/132</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="markdown"><span class="p">-</span> Dont fill in gaps in parent with bases from child <span class="p">[</span><span class="nv" style="color: #008080;">\#131</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/131</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.2.0](https://github.com/sanger-pathogens/gubbins/tree/v1.2.0) (2015-03-06)</span></span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.1.2...v1.2.0</span><span class="p">)</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.1.2](https://github.com/sanger-pathogens/gubbins/tree/v1.1.2) (2015-03-06)</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.1.1...v1.1.2</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="markdown"></span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="markdown"><span class="p">-</span> Update robustness <span class="p">[</span><span class="nv" style="color: #008080;">\#128</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/128</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="markdown"><span class="p">-</span> message about invalid outgroups <span class="p">[</span><span class="nv" style="color: #008080;">\#127</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/127</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.1.1](https://github.com/sanger-pathogens/gubbins/tree/v1.1.1) (2015-01-23)</span></span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.1.0...v1.1.1</span><span class="p">)</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="markdown"><span class="p">-</span> Clade as outgroup <span class="p">[</span><span class="nv" style="color: #008080;">\#126</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/126</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.1.0](https://github.com/sanger-pathogens/gubbins/tree/v1.1.0) (2015-01-23)</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.12...v1.1.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.12](https://github.com/sanger-pathogens/gubbins/tree/v1.0.12) (2015-01-20)</span></span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.11...v1.0.12</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="markdown"><span class="p">-</span> test data <span class="p">[</span><span class="nv" style="color: #008080;">\#125</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/125</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="markdown"><span class="p">-</span> Remove internal nodes from final tree <span class="p">[</span><span class="nv" style="color: #008080;">\#124</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/124</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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">
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.11](https://github.com/sanger-pathogens/gubbins/tree/v1.0.11) (2015-01-19)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.10...v1.0.11</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="markdown"></span>
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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="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="markdown"></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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<pre style="margin: 0;">+<span id="LC367" class="line" lang="markdown"><span class="p">-</span> check fasta files valid and check for intermediate raxml files <span class="p">[</span><span class="nv" style="color: #008080;">\#123</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/123</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</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="markdown"></span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.10](https://github.com/sanger-pathogens/gubbins/tree/v1.0.10) (2015-01-19)</span></span>
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.9...v1.0.10</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="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.9](https://github.com/sanger-pathogens/gubbins/tree/v1.0.9) (2015-01-06)</span></span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/1.0.9...v1.0.9</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.0.9](https://github.com/sanger-pathogens/gubbins/tree/1.0.9) (2015-01-06)</span></span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.8...1.0.9</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="markdown"></span>
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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="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="markdown"></span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="markdown"><span class="p">-</span> Dont use cpu info to find the flags <span class="p">[</span><span class="nv" style="color: #008080;">\#122</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/122</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</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="markdown"><span class="p">-</span> class namespace <span class="p">[</span><span class="nv" style="color: #008080;">\#121</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/121</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.8](https://github.com/sanger-pathogens/gubbins/tree/v1.0.8) (2014-12-08)</span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.7...v1.0.8</span><span class="p">)</span></span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="markdown"></span>
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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="markdown"><span class="p">-</span> reduced functionality but more stable cpu info lookup <span class="p">[</span><span class="nv" style="color: #008080;">\#120</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/120</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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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<pre style="margin: 0;">+<span id="LC389" class="line" lang="markdown"><span class="p">-</span> Rho theta <span class="p">[</span><span class="nv" style="color: #008080;">\#119</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/119</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</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="markdown"></span>
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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">
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.7](https://github.com/sanger-pathogens/gubbins/tree/v1.0.7) (2014-12-08)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.6...v1.0.7</span><span class="p">)</span></span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="markdown"></span>
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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="markdown"><span class="p">-</span> allow for variation and exclude zero track length <span class="p">[</span><span class="nv" style="color: #008080;">\#118</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/118</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</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="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.6](https://github.com/sanger-pathogens/gubbins/tree/v1.0.6) (2014-12-03)</span></span>
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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
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.5...v1.0.6</span><span class="p">)</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="markdown"></span>
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<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
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.5](https://github.com/sanger-pathogens/gubbins/tree/v1.0.5) (2014-11-19)</span></span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.2...v1.0.5</span><span class="p">)</span></span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="markdown"></span>
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<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
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="markdown"></span>
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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
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="markdown"><span class="p">-</span> fasttree executables with titlecase and lowercase <span class="p">[</span><span class="nv" style="color: #008080;">\#117</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/117</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="markdown"><span class="p">-</span> warning message when changing number of threads <span class="p">[</span><span class="nv" style="color: #008080;">\#116</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/116</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="markdown"><span class="p">-</span> Change raxml exec search order <span class="p">[</span><span class="nv" style="color: #008080;">\#115</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/115</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.2](https://github.com/sanger-pathogens/gubbins/tree/v1.0.2) (2014-10-16)</span></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0.1...v1.0.2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="markdown"><span class="p">-</span> rename convergence methods and allow for more <span class="p">[</span><span class="nv" style="color: #008080;">\#114</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/114</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0.1](https://github.com/sanger-pathogens/gubbins/tree/v1.0.1) (2014-10-14)</span></span>
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v1.0...v1.0.1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="markdown"><span class="p">-</span> unstable test fixed <span class="p">[</span><span class="nv" style="color: #008080;">\#113</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/113</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v1.0](https://github.com/sanger-pathogens/gubbins/tree/v1.0) (2014-10-14)</span></span>
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/0.6...v1.0</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="markdown"><span class="p">-</span> Converging recombinations <span class="p">[</span><span class="nv" style="color: #008080;">\#112</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/112</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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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">
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.6](https://github.com/sanger-pathogens/gubbins/tree/0.6) (2014-09-24)</span></span>
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/0.7...0.6</span><span class="p">)</span></span>
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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">
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.7](https://github.com/sanger-pathogens/gubbins/tree/0.7) (2014-09-24)</span></span>
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435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v0.6...0.7</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="437" style="width: 35px; color: rgba(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="LC437" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.6](https://github.com/sanger-pathogens/gubbins/tree/v0.6) (2014-09-09)</span></span>
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v0.5...v0.6</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="markdown"><span class="p">-</span> Gubbins drawer can use recombination embl file <span class="p">[</span><span class="nv" style="color: #008080;">\#111</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/111</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="444" style="width: 35px; color: rgba(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="LC444" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.5](https://github.com/sanger-pathogens/gubbins/tree/v0.5) (2014-09-09)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="445" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v0.4.1...v0.5</span><span class="p">)</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="markdown"><span class="p">-</span> thread support for raxml <span class="p">[</span><span class="nv" style="color: #008080;">\#110</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/110</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="451" style="width: 35px; color: rgba(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="LC451" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.4.1](https://github.com/sanger-pathogens/gubbins/tree/v0.4.1) (2014-09-08)</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v0.4...v0.4.1</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="markdown"><span class="p">-</span> Check for lowercase fasttree exec <span class="p">[</span><span class="nv" style="color: #008080;">\#109</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/109</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.4](https://github.com/sanger-pathogens/gubbins/tree/v0.4) (2014-09-05)</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/v0.3...v0.4</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="markdown"><span class="p">-</span> pairwise rename output files <span class="p">[</span><span class="nv" style="color: #008080;">\#108</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/108</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="markdown"><span class="p">-</span> Update stats headers <span class="p">[</span><span class="nv" style="color: #008080;">\#107</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/107</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [v0.3](https://github.com/sanger-pathogens/gubbins/tree/v0.3) (2014-09-04)</span></span>
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/0.2...v0.3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.2](https://github.com/sanger-pathogens/gubbins/tree/0.2) (2014-09-02)</span></span>
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/0.1.11...0.2</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="markdown"><span class="p">-</span> Catch too few sequences <span class="p">[</span><span class="nv" style="color: #008080;">\#106</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/106</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<td class="diff-line-num new new_line" data-linenumber="476" style="width: 35px; color: rgba(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="LC476" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.1.11](https://github.com/sanger-pathogens/gubbins/tree/0.1.11) (2014-08-22)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="477" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/0.1.10...0.1.11</span><span class="p">)</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="479" style="width: 35px; color: rgba(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="LC479" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="481" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="markdown"><span class="p">-</span> version in configure <span class="p">[</span><span class="nv" style="color: #008080;">\#105</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/105</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="markdown"><span class="p">-</span> Support for bipartition trees as input <span class="p">[</span><span class="nv" style="color: #008080;">\#104</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/104</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="484" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.1.10](https://github.com/sanger-pathogens/gubbins/tree/0.1.10) (2014-08-22)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="485" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/0.1.9...0.1.10</span><span class="p">)</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="markdown"></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="489" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="markdown"><span class="p">-</span> print list of excluded sequences <span class="p">[</span><span class="nv" style="color: #008080;">\#103</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/103</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="491" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.1.9](https://github.com/sanger-pathogens/gubbins/tree/0.1.9) (2014-08-22)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/0.1.8...0.1.9</span><span class="p">)</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="markdown"></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="markdown"><span class="p">-</span> print errors for invalid input files <span class="p">[</span><span class="nv" style="color: #008080;">\#102</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/102</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.1.8](https://github.com/sanger-pathogens/gubbins/tree/0.1.8) (2014-08-15)</span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/0.1.7...0.1.8</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="markdown"></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="markdown"><span class="p">-</span> Fasttree exec <span class="p">[</span><span class="nv" style="color: #008080;">\#101</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/101</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="markdown"></span>
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<td class="diff-line-num new new_line" data-linenumber="505" style="width: 35px; color: rgba(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="LC505" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.1.7](https://github.com/sanger-pathogens/gubbins/tree/0.1.7) (2014-08-14)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">Full Changelog</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/compare/0.1.6...0.1.7</span><span class="p">)</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="markdown"></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="markdown"></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="markdown"><span class="p">-</span> Build for trusty <span class="p">[</span><span class="nv" style="color: #008080;">\#100</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/100</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="markdown"></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [0.1.6](https://github.com/sanger-pathogens/gubbins/tree/0.1.6) (2014-08-12)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">**Merged pull requests:**</span></span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="markdown"></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="markdown"><span class="p">-</span> Changes from Aidan Delaney <span class="p">[</span><span class="nv" style="color: #008080;">\#99</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/99</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="markdown"><span class="p">-</span> Stats missing snps <span class="p">[</span><span class="nv" style="color: #008080;">\#98</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/98</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="markdown"><span class="p">-</span> update no support option in fastml <span class="p">[</span><span class="nv" style="color: #008080;">\#97</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/97</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="markdown"><span class="p">-</span> move blocks inwards <span class="p">[</span><span class="nv" style="color: #008080;">\#96</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/96</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="markdown"><span class="p">-</span> define is starting tree method as static <span class="p">[</span><span class="nv" style="color: #008080;">\#95</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/95</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="markdown"><span class="p">-</span> starting tree needed to come from args <span class="p">[</span><span class="nv" style="color: #008080;">\#94</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/94</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="markdown"><span class="p">-</span> Python tests <span class="p">[</span><span class="nv" style="color: #008080;">\#93</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/93</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="markdown"><span class="p">-</span> remove duplicate move <span class="p">[</span><span class="nv" style="color: #008080;">\#92</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/92</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="markdown"><span class="p">-</span> dont move in twice <span class="p">[</span><span class="nv" style="color: #008080;">\#91</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/91</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="markdown"><span class="p">-</span> typo in method, too many args <span class="p">[</span><span class="nv" style="color: #008080;">\#90</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/90</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="markdown"><span class="p">-</span> move end block in correct number of snps <span class="p">[</span><span class="nv" style="color: #008080;">\#89</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/89</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="markdown"><span class="p">-</span> Span gaps <span class="p">[</span><span class="nv" style="color: #008080;">\#88</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/88</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="markdown"><span class="p">-</span> translate snps and gaps to original genome space coords <span class="p">[</span><span class="nv" style="color: #008080;">\#87</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/87</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="markdown"><span class="p">-</span> extend blocks over gaps <span class="p">[</span><span class="nv" style="color: #008080;">\#86</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/86</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="markdown"><span class="p">-</span> dont call methods and variables the same thing <span class="p">[</span><span class="nv" style="color: #008080;">\#85</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/85</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="markdown"><span class="p">-</span> remove latest tree symlink if it exists, even if its broken <span class="p">[</span><span class="nv" style="color: #008080;">\#84</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/84</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="markdown"><span class="p">-</span> delete intermediate raxml files <span class="p">[</span><span class="nv" style="color: #008080;">\#83</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/83</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="markdown"><span class="p">-</span> Eliminate memory leaks and uninitalised reads/writes <span class="p">[</span><span class="nv" style="color: #008080;">\#82</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/82</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="markdown"><span class="p">-</span> GPL <span class="p">[</span><span class="nv" style="color: #008080;">\#81</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/81</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="markdown"><span class="p">-</span> reduce memory usage and fix seg fault <span class="p">[</span><span class="nv" style="color: #008080;">\#80</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/80</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="markdown"><span class="p">-</span> move math lib linking to end <span class="p">[</span><span class="nv" style="color: #008080;">\#79</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/79</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="markdown"><span class="p">-</span> move zlib linking to end <span class="p">[</span><span class="nv" style="color: #008080;">\#78</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/78</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="markdown"><span class="p">-</span> swap output suppression <span class="p">[</span><span class="nv" style="color: #008080;">\#77</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/77</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="markdown"><span class="p">-</span> memory leaks <span class="p">[</span><span class="nv" style="color: #008080;">\#76</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/76</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="markdown"><span class="p">-</span> update window creation <span class="p">[</span><span class="nv" style="color: #008080;">\#75</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/75</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="markdown"><span class="p">-</span> part4 log10 <span class="p">[</span><span class="nv" style="color: #008080;">\#74</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/74</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="markdown"><span class="p">-</span> Improving likelihood <span class="p">[</span><span class="nv" style="color: #008080;">\#73</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/73</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="markdown"><span class="p">-</span> Improving likelihood <span class="p">[</span><span class="nv" style="color: #008080;">\#72</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/72</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="markdown"><span class="p">-</span> reroot on outgroup should keep internal nodes <span class="p">[</span><span class="nv" style="color: #008080;">\#71</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/71</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="markdown"><span class="p">-</span> Use bases for gaps for internal nodes after fastml <span class="p">[</span><span class="nv" style="color: #008080;">\#70</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/70</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="markdown"><span class="p">-</span> propagate unambiguous bases up the tree <span class="p">[</span><span class="nv" style="color: #008080;">\#69</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/69</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="markdown"><span class="p">-</span> move inwards one at a time, remove gap extending, Bonferroni correction, sliding window 1 <span class="p">[</span><span class="nv" style="color: #008080;">\#68</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/68</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="markdown"><span class="p">-</span> new window shifting method and bug with detecting snps <span class="p">[</span><span class="nv" style="color: #008080;">\#67</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/67</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="markdown"><span class="p">-</span> dont move window past size of genome <span class="p">[</span><span class="nv" style="color: #008080;">\#66</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/66</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="markdown"><span class="p">-</span> move window in to first snp <span class="p">[</span><span class="nv" style="color: #008080;">\#65</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/65</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="markdown"><span class="p">-</span> Updates to coords other minor bugs <span class="p">[</span><span class="nv" style="color: #008080;">\#64</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/64</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="markdown"><span class="p">-</span> sliding window at half minimum window size <span class="p">[</span><span class="nv" style="color: #008080;">\#63</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/63</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="markdown"><span class="p">-</span> swap bases in snp tab file and cleanup filenames <span class="p">[</span><span class="nv" style="color: #008080;">\#62</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/62</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="markdown"><span class="p">-</span> Gaps can be in ref as well as alt <span class="p">[</span><span class="nv" style="color: #008080;">\#61</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/61</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="markdown"><span class="p">-</span> pairwise <span class="p">[</span><span class="nv" style="color: #008080;">\#60</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/60</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="markdown"><span class="p">-</span> remove filtered sequences from starting tree <span class="p">[</span><span class="nv" style="color: #008080;">\#59</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/59</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="markdown"><span class="p">-</span> missing comma <span class="p">[</span><span class="nv" style="color: #008080;">\#58</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/58</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="markdown"><span class="p">-</span> unquote tree nodes for fastml and check if too much is filtered out <span class="p">[</span><span class="nv" style="color: #008080;">\#57</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/57</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="markdown"><span class="p">-</span> update test files <span class="p">[</span><span class="nv" style="color: #008080;">\#56</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/56</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="markdown"><span class="p">-</span> Fastml no gaps <span class="p">[</span><span class="nv" style="color: #008080;">\#55</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/55</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="markdown"><span class="p">-</span> readme <span class="p">[</span><span class="nv" style="color: #008080;">\#54</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/54</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="markdown"><span class="p">-</span> snp branch output and prefiltering aln <span class="p">[</span><span class="nv" style="color: #008080;">\#53</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/53</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="markdown"><span class="p">-</span> make drawer work with empty tracks <span class="p">[</span><span class="nv" style="color: #008080;">\#52</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/52</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="markdown"><span class="p">-</span> strip off input params when testing if exec is in path <span class="p">[</span><span class="nv" style="color: #008080;">\#51</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/51</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="markdown"><span class="p">-</span> Fastml integration <span class="p">[</span><span class="nv" style="color: #008080;">\#50</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/50</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="markdown"><span class="p">-</span> versioning <span class="p">[</span><span class="nv" style="color: #008080;">\#48</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/48</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="markdown"><span class="p">-</span> Cleanup intermediate files <span class="p">[</span><span class="nv" style="color: #008080;">\#47</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/47</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</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="markdown"><span class="p">-</span> treat N in the same way as gaps when snp searching <span class="p">[</span><span class="nv" style="color: #008080;">\#46</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/46</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="markdown"><span class="p">-</span> Treat N as gap when extending over gaps at block boundries <span class="p">[</span><span class="nv" style="color: #008080;">\#45</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/45</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="markdown"><span class="p">-</span> use same fasttree params in hybrid <span class="p">[</span><span class="nv" style="color: #008080;">\#44</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/44</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="markdown"><span class="p">-</span> vcf coords start from 1 <span class="p">[</span><span class="nv" style="color: #008080;">\#43</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/43</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="markdown"><span class="p">-</span> unquote strings <span class="p">[</span><span class="nv" style="color: #008080;">\#42</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/42</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="markdown"><span class="p">-</span> default preserve underscores to true <span class="p">[</span><span class="nv" style="color: #008080;">\#41</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/41</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="markdown"><span class="p">-</span> preserve underscores <span class="p">[</span><span class="nv" style="color: #008080;">\#40</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/40</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="markdown"><span class="p">-</span> Reroot around edge <span class="p">[</span><span class="nv" style="color: #008080;">\#39</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/39</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="markdown"><span class="p">-</span> remove calls to reading beginnign of line <span class="p">[</span><span class="nv" style="color: #008080;">\#38</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/38</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="markdown"><span class="p">-</span> Read line memory leak <span class="p">[</span><span class="nv" style="color: #008080;">\#37</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/37</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="markdown"><span class="p">-</span> increase read line memory <span class="p">[</span><span class="nv" style="color: #008080;">\#36</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/36</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="markdown"><span class="p">-</span> resize read line buffer <span class="p">[</span><span class="nv" style="color: #008080;">\#35</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/35</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="markdown"><span class="p">-</span> Copyfile <span class="p">[</span><span class="nv" style="color: #008080;">\#34</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/34</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="markdown"><span class="p">-</span> increase read buffer size <span class="p">[</span><span class="nv" style="color: #008080;">\#33</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/33</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="markdown"><span class="p">-</span> semi colon at end of tree <span class="p">[</span><span class="nv" style="color: #008080;">\#32</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/32</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="markdown"><span class="p">-</span> speedup gubbins <span class="p">[</span><span class="nv" style="color: #008080;">\#31</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/31</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="markdown"><span class="p">-</span> scale distances by num snps <span class="p">[</span><span class="nv" style="color: #008080;">\#30</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/30</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="markdown"><span class="p">-</span> providing a starting tree skips first tree building step <span class="p">[</span><span class="nv" style="color: #008080;">\#29</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/29</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="markdown"><span class="p">-</span> calc bases in recombs <span class="p">[</span><span class="nv" style="color: #008080;">\#28</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/28</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="markdown"><span class="p">-</span> improved stats <span class="p">[</span><span class="nv" style="color: #008080;">\#27</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/27</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="markdown"><span class="p">-</span> calc snp stats and parameter to set min snps <span class="p">[</span><span class="nv" style="color: #008080;">\#26</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/26</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="markdown"><span class="p">-</span> Get all gaps <span class="p">[</span><span class="nv" style="color: #008080;">\#25</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/25</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="markdown"><span class="p">-</span> increase window size to 20k <span class="p">[</span><span class="nv" style="color: #008080;">\#24</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/24</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="markdown"><span class="p">-</span> Span gaps <span class="p">[</span><span class="nv" style="color: #008080;">\#23</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/23</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="markdown"><span class="p">-</span> fasttree needs to use output of gubbins <span class="p">[</span><span class="nv" style="color: #008080;">\#22</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/22</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="markdown"><span class="p">-</span> extend blocks over gaps <span class="p">[</span><span class="nv" style="color: #008080;">\#21</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/21</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="markdown"><span class="p">-</span> raxml exec check <span class="p">[</span><span class="nv" style="color: #008080;">\#20</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/20</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="markdown"><span class="p">-</span> Merge blocks straddling gaps <span class="p">[</span><span class="nv" style="color: #008080;">\#19</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/19</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="markdown"><span class="p">-</span> fix remove <span class="p">[</span><span class="nv" style="color: #008080;">\#18</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/18</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="markdown"><span class="p">-</span> speedup phylip file writing second try <span class="p">[</span><span class="nv" style="color: #008080;">\#17</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/17</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="markdown"><span class="p">-</span> speedup phylip file writing <span class="p">[</span><span class="nv" style="color: #008080;">\#16</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/16</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="markdown"><span class="p">-</span> provide alignment filename not full path for fastree <span class="p">[</span><span class="nv" style="color: #008080;">\#15</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/15</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="markdown"><span class="p">-</span> remove hardcoded path to exec <span class="p">[</span><span class="nv" style="color: #008080;">\#14</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/14</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="markdown"><span class="p">-</span> rerun autoreconf <span class="p">[</span><span class="nv" style="color: #008080;">\#13</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/13</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="markdown"><span class="p">-</span> midpoint rerooting and pairwise comparison <span class="p">[</span><span class="nv" style="color: #008080;">\#12</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/12</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="markdown"><span class="p">-</span> Use get opt long <span class="p">[</span><span class="nv" style="color: #008080;">\#11</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/11</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="markdown"><span class="p">-</span> dont point to gubbins in same dir <span class="p">[</span><span class="nv" style="color: #008080;">\#10</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/10</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="markdown"><span class="p">-</span> dont print out rerooted tree to stdout <span class="p">[</span><span class="nv" style="color: #008080;">\#9</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/9</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="markdown"><span class="p">-</span> Hybrid tree building <span class="p">[</span><span class="nv" style="color: #008080;">\#8</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/8</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="markdown"><span class="p">-</span> Rewrite perl as python <span class="p">[</span><span class="nv" style="color: #008080;">\#7</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/7</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="markdown"><span class="p">-</span> send in most recent phylip file to raxml <span class="p">[</span><span class="nv" style="color: #008080;">\#6</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/6</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</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="markdown"><span class="p">-</span> run gubbins original snp sites <span class="p">[</span><span class="nv" style="color: #008080;">\#5</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/5</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="markdown"><span class="p">-</span> run gubbins with original snp sites <span class="p">[</span><span class="nv" style="color: #008080;">\#4</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/4</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="markdown"><span class="p">-</span> Gubbins overall tests <span class="p">[</span><span class="nv" style="color: #008080;">\#3</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/3</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="markdown"><span class="p">-</span> Fix memory leak and properly remove recombinations <span class="p">[</span><span class="nv" style="color: #008080;">\#2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/2</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="markdown"><span class="p">-</span> dont ignore internal nodes <span class="p">[</span><span class="nv" style="color: #008080;">\#1</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/pull/1</span><span class="p">)</span> <span class="p">(</span><span class="sx" style="color: #d14;">[andrewjpage](https://github.com/andrewjpage</span><span class="p">)</span>)</span>
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="markdown"><span class="se" style="color: #d14;">\*</span> <span class="ge" style="font-style: italic;">*This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*</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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/gubbins/commit/490cb88e0c973df3eb02e7e7b3d8e71ee1a80f75#6651ddff6eb82c840ced7c1dddee15c6e1913dd4"><strong>Dockerfile</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" 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">@@ -68,6 +68,3 @@ RUN git clone https://github.com/sanger-pathogens/gubbins.git \</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> make <span class="nb" style="color: #0086b3;">install</span> <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> <span class="nb" style="color: #0086b3;">cd </span>python <span class="se" style="color: #d14;">\</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="docker"> <span class="o" style="font-weight: 600;">&&</span> python3 setup.py <span class="nb" style="color: #0086b3;">install</span></span></pre>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="docker"> </span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="docker"><span class="c" style="color: #998; font-style: italic;"># Rename executable for backwards compatibility</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="docker"><span class="k" style="font-weight: 600;">RUN </span><span class="nb" style="color: #0086b3;">mv</span> /usr/local/bin/run_gubbins.py /usr/local/bin/run_gubbins</span></pre>
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<a href="https://salsa.debian.org/med-team/gubbins/commit/490cb88e0c973df3eb02e7e7b3d8e71ee1a80f75#b2270542d41297db1ee0d12698e609ea3ec25ce7"><strong>INSTALL.md</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown">Before you do anything, please have a look at the <span class="p">[</span><span class="nv" style="color: #008080;">Gubbins webpage</span><span class="p">](</span><span class="sx" style="color: #d14;">http://sanger-pathogens.github.io/gubbins/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #999;"># Installation</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">There are a few ways to install Gubbins and its dependencies. The simpliest way is using conda.</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="markdown"><span class="p">*</span> OSX/Linux - Bioconda</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">*</span> Linux - Ubuntu Xenial (16.04) & Debian (unstable)</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="p">*</span> OSX/Linux/Cloud/Windows - Docker</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="p">*</span> OSX/Linux - from source</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="p">*</span> OSX/Linux/Windows - Virtual Machine</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## OSX/Linux - conda</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown">Install conda and enable the bioconda channels.</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="diff-line-num old old_line" data-linenumber="16" 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="LC16" class="line" lang="markdown">conda config --add channels r</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown">conda config --add channels defaults</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown">conda config --add channels conda-forge</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown">conda config --add channels bioconda</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown">conda install gubbins</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Linux - Ubuntu Xenial (16.04) & Debian (unstable)</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown">Gubbins has been packaged by the Debian Med team and is trivial to install using apt.</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown"><span class="sb" style="color: #d14;"> sudo apt-get install gubbins</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## OSX/Linux/Cloud/Windows - Docker</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown">We have a docker container which gets automatically built from the latest version of Gubbins in Debian Med. To install it:</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"><span class="sb" style="color: #d14;"> docker pull sangerpathogens/gubbins</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown">To use it you would use a command such as this:</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown"><span class="sb" style="color: #d14;"> docker run --rm -it -v <local_dir>:<remote_dir> sangerpathogens/gubbins run_gubbins -p <remote_dir>/<prefix> [<options>] <remote_dir>/<alignment_file></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown">The flag <span class="sb" style="color: #d14;">`-v`</span> synchronizes a directory on the host machine (here denoted as <span class="sb" style="color: #d14;">`<local_dir>`</span>) with a directory in the Docker container (here denoted as <span class="sb" style="color: #d14;">`<remote_dir>`</span>).</span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"><span class="sb" style="color: #d14;">`<remote_dir>`</span> does not need to exist in the container before the run, a common choice is <span class="sb" style="color: #d14;">`/data`</span>.</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown">Note that both <span class="sb" style="color: #d14;">`<local_dir>`</span> and <span class="sb" style="color: #d14;">`<remote_dir>`</span> must be absolute paths.</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown">The input alignment file must be present in <span class="sb" style="color: #d14;">`<local_dir>`</span> (or in one of its subdirectories).</span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown">In order to retrieve the files produced by Gubbins, run the program with option <span class="sb" style="color: #d14;">`-p`</span>; </span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown">the argument of this option must consist of <span class="sb" style="color: #d14;">`<remote_dir>`</span>, followed by an arbitrary identifier (here denoted as <span class="sb" style="color: #d14;">`<prefix>`</span>).</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## OSX/Linux - from source</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown">This is the most difficult method and is only suitable for someone with advanced computing skills. Please consider using Conda instead.</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown">Install the dependencies and include them in your <span class="sb" style="color: #d14;">`PATH`</span>:</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">FastTree</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.microbesonline.org/fasttree/#Install</span><span class="p">)</span> <span class="p">(</span> <span class="sx" style="color: #d14;">>=2.1.4</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">RAxML</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/stamatak/standard-RAxML</span><span class="p">)</span> <span class="p">(</span> <span class="sx" style="color: #d14;">>=8.0</span> <span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"><span class="p">*</span> Python modules: Biopython (> 1.59), DendroPy (>=4.0), Reportlab, nose, pillow</span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown"><span class="p">*</span> Standard build environment tools (e.g. python3, pip3, make, autoconf, libtool, gcc, check, etc...)</span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown">Clone or download the source code from GitHub and run the following commands to install Gubbins:</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown">autoreconf -i</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown">./configure [--prefix=$PREFIX]</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="markdown">make</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown">[sudo] make install</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="markdown">cd python</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="markdown">[sudo] python3 setup.py install</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown">Use <span class="sb" style="color: #d14;">`sudo`</span> to install Gubbins system-wide. If you don't have the permissions, run <span class="sb" style="color: #d14;">`configure`</span> with a prefix to install Gubbins in your home directory.</span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## OSX/Linux/Windows - Virtual Machine</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="markdown">Roary wont run natively on Windows but we have created a virtual machine which has all of the software setup, along with the test datasets from the paper. </span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="markdown">It is based on <span class="p">[</span><span class="nv" style="color: #008080;">Bio-Linux 8</span><span class="p">](</span><span class="sx" style="color: #d14;">http://environmentalomics.org/bio-linux/</span><span class="p">)</span>. You need to first install <span class="p">[</span><span class="nv" style="color: #008080;">VirtualBox</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.virtualbox.org/</span><span class="p">)</span>, </span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="markdown">then load the virtual machine, using the 'File -> Import Appliance' menu option. The root password is 'manager'.</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="markdown"><span class="p">*</span> ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="markdown">More importantly though, if your trying to do bioinformatics on Windows, your not going to get very far and you should seriously consider upgrading to Linux.</span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown"></span></pre>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/gubbins/commit/490cb88e0c973df3eb02e7e7b3d8e71ee1a80f75#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown">Please see our website for more information on <span class="p">[</span><span class="nv" style="color: #008080;">Gubbins</span><span class="p">](</span><span class="sx" style="color: #d14;">http://sanger-pathogens.github.io/gubbins/</span><span class="p">)</span> or read our paper:</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Gubbins</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown">Genealogies Unbiased By recomBinations In Nucleotide Sequences </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown">PLEASE NOTE: we currently do not have the resources to provide support for Gubbins, so please do not expect a reply if you flag any issue.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Unmaintained</span><span class="p">](</span><span class="sx" style="color: #d14;">http://unmaintained.tech/badge.svg</span><span class="p">)</span>](http://unmaintained.tech/) </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/gubbins.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/gubbins) </span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![License: GPL v2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/License-GPL%20v2-brightgreen.svg</span><span class="p">)</span>](https://github.com/sanger-pathogens/gubbins/blob/master/LICENSE) </span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/NAR-10.1093-brightgreen.svg</span><span class="p">)</span>](https://academic.oup.com/nar/article/43/3/e15/2410982) </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg</span><span class="p">)</span>](http://bioconda.github.io/recipes/gubbins/README.html) </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Container ready</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/container-ready-brightgreen.svg</span><span class="p">)</span>](https://quay.io/repository/biocontainers/gubbins) </span>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Docker Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/docker/build/sangerpathogens/gubbins.svg</span><span class="p">)</span>](https://hub.docker.com/r/sangerpathogens/gubbins) </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Docker Pulls</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/docker/pulls/sangerpathogens/gubbins.svg</span><span class="p">)</span>](https://hub.docker.com/r/sangerpathogens/gubbins) </span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![codecov</span><span class="p">](</span><span class="sx" style="color: #d14;">https://codecov.io/gh/sanger-pathogens/gubbins/branch/master/graph/badge.svg</span><span class="p">)</span>](https://codecov.io/gh/sanger-pathogens/gubbins)</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Contents</span></span>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Introduction</span><span class="p">](</span><span class="sx" style="color: #d14;">#introduction</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Installation</span><span class="p">](</span><span class="sx" style="color: #d14;">#installation</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Required dependencies</span><span class="p">](</span><span class="sx" style="color: #d14;">#required-dependencies</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">OSX/Linux \- conda</span><span class="p">](</span><span class="sx" style="color: #d14;">#osxlinux---conda</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Linux \- Ubuntu Xenial (16\.04) & Debian (unstable)</span><span class="p">](</span><span class="sx" style="color: #d14;">#linux---ubuntu-xenial-1604--debian-unstable</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">OSX/Linux/Cloud/Windows \- Docker</span><span class="p">](</span><span class="sx" style="color: #d14;">#osxlinuxcloudwindows---docker</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="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">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">OSX/Linux \- from source</span><span class="p">](</span><span class="sx" style="color: #d14;">#osxlinux---from-source</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_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">
25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">OSX/Linux/Windows \- Virtual Machine</span><span class="p">](</span><span class="sx" style="color: #d14;">#osxlinuxwindows---virtual-machine</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Running the tests</span><span class="p">](</span><span class="sx" style="color: #d14;">#running-the-tests</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Usage</span><span class="p">](</span><span class="sx" style="color: #d14;">#usage</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Generating Input files</span><span class="p">](</span><span class="sx" style="color: #d14;">#generating-input-files</span><span class="p">)</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(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="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="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Output files</span><span class="p">](</span><span class="sx" style="color: #d14;">#output-files</span><span class="p">)</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">License</span><span class="p">](</span><span class="sx" style="color: #d14;">#license</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Feedback/Issues</span><span class="p">](</span><span class="sx" style="color: #d14;">#feedbackissues</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Citation</span><span class="p">](</span><span class="sx" style="color: #d14;">#citation</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Further Information</span><span class="p">](</span><span class="sx" style="color: #d14;">#further-information</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Data from the paper</span><span class="p">](</span><span class="sx" style="color: #d14;">#data-from-the-paper</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Midpoint rerooting</span><span class="p">](</span><span class="sx" style="color: #d14;">#midpoint-rerooting</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p"> *</span> <span class="p">[</span><span class="nv" style="color: #008080;">Ancestral sequence reconstruction</span><span class="p">](</span><span class="sx" style="color: #d14;">#ancestral-sequence-reconstruction</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Introduction</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown">Since the introduction of high-throughput, second-generation DNA sequencing technologies, there has been an enormous increase in the size of datasets being used for estimating bacterial population phylodynamics. Although many phylogenetic techniques are scalable to hundreds of bacterial genomes, methods which have been used for mitigating the effect of mechanisms of horizontal sequence transfer on phylogenetic reconstructions cannot cope with these new datasets. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown">"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". doi:10.1093/nar/gku1196, Nucleic Acids Research, 2014.]</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="markdown">(http://nar.oxfordjournals.org/content/43/3/e15)</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Installation</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown">Before you do anything, please have a look at the <span class="p">[</span><span class="nv" style="color: #008080;">Gubbins webpage</span><span class="p">](</span><span class="sx" style="color: #d14;">http://sanger-pathogens.github.io/gubbins/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Gubbins</span></span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=======</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Required dependencies</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">FastTree</span><span class="p">](</span><span class="sx" style="color: #d14;">http://www.microbesonline.org/fasttree/#Install</span><span class="p">)</span> <span class="p">(</span> <span class="sx" style="color: #d14;">>=2.1.4</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown"><span class="p">*</span> <span class="p">[</span><span class="nv" style="color: #008080;">RAxML</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/stamatak/standard-RAxML</span><span class="p">)</span> <span class="p">(</span> <span class="sx" style="color: #d14;">>=8.0</span> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown"><span class="p">*</span> Python modules: Biopython (> 1.59), DendroPy (>=4.0), Reportlab, nose, pillow</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">*</span> Standard build environment tools (e.g. python3, pip3, make, autoconf, libtool, gcc, check, etc...)</span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Build Status</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/sanger-pathogens/gubbins.svg?branch=master</span><span class="p">)</span>](https://travis-ci.org/sanger-pathogens/gubbins)</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">There are a number of ways to install Gubbins and details are provided below. If you encounter an issue when installing Gubbins please contact your local system administrator.</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### OSX/Linux - conda</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown">Install conda and enable the bioconda channels.</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="markdown">conda config --add channels r</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">conda config --add channels defaults</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown">conda config --add channels conda-forge</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown">conda config --add channels bioconda</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown">conda install gubbins</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Linux - Ubuntu Xenial (16.04) & Debian (unstable)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">Gubbins has been packaged by the Debian Med team and is trivial to install using apt.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown"><span class="sb" style="color: #d14;"> sudo apt-get install gubbins</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### OSX/Linux/Cloud/Windows - Docker</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown">We have a docker container which gets automatically built from the latest version of Gubbins in Debian Med. To install it:</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"><span class="sb" style="color: #d14;"> docker pull sangerpathogens/gubbins</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="markdown">To use it you would use a command such as this:</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="markdown"><span class="sb" style="color: #d14;"> docker run --rm -it -v <local_dir>:<remote_dir> sangerpathogens/gubbins run_gubbins -p <remote_dir>/<prefix> [<options>] <remote_dir>/<alignment_file></span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="markdown">The flag <span class="sb" style="color: #d14;">`-v`</span> synchronizes a directory on the host machine (here denoted as <span class="sb" style="color: #d14;">`<local_dir>`</span>) with a directory in the Docker container (here denoted as <span class="sb" style="color: #d14;">`<remote_dir>`</span>).</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="markdown"><span class="sb" style="color: #d14;">`<remote_dir>`</span> does not need to exist in the container before the run, a common choice is <span class="sb" style="color: #d14;">`/data`</span>.</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="markdown">Note that both <span class="sb" style="color: #d14;">`<local_dir>`</span> and <span class="sb" style="color: #d14;">`<remote_dir>`</span> must be absolute paths.</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="markdown">The input alignment file must be present in <span class="sb" style="color: #d14;">`<local_dir>`</span> (or in one of its subdirectories).</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="markdown">In order to retrieve the files produced by Gubbins, run the program with option <span class="sb" style="color: #d14;">`-p`</span>; </span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="markdown">the argument of this option must consist of <span class="sb" style="color: #d14;">`<remote_dir>`</span>, followed by an arbitrary identifier (here denoted as <span class="sb" style="color: #d14;">`<prefix>`</span>).</span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">Since the introduction of high-throughput, second-generation DNA sequencing technologies, there has been an enormous increase in the size of datasets being used for estimating bacterial population phylodynamics. Although many phylogenetic techniques are scalable to hundreds of bacterial genomes, methods which have been used for mitigating the effect of mechanisms of horizontal sequence transfer on phylogenetic reconstructions cannot cope with these new datasets. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.</span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Install</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">=======</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown">Please see the <span class="p">[</span><span class="nv" style="color: #008080;">INSTALL</span><span class="p">](</span><span class="sx" style="color: #d14;">INSTALL.md</span><span class="p">)</span> file for detailed instructions.</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### OSX/Linux - from source</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="markdown">This is the most difficult method and is only suitable for someone with advanced computing skills. Please consider using Conda instead.</span>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown"></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Running Gubbins</span></span>
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19
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">===============</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="markdown">Install the dependencies and include them in your <span class="sb" style="color: #d14;">`PATH`</span>.</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown">Clone or download the source code from GitHub and run the following commands to install Gubbins:</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="markdown">autoreconf -i</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="markdown">./configure [--prefix=$PREFIX]</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="markdown">make</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="markdown">[sudo] make install</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="markdown">cd python</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="markdown">[sudo] python3 setup.py install</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="markdown">Use <span class="sb" style="color: #d14;">`sudo`</span> to install Gubbins system-wide. If you don't have the permissions, run <span class="sb" style="color: #d14;">`configure`</span> with a prefix to install Gubbins in your home directory.</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### OSX/Linux/Windows - Virtual Machine</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="markdown">Gubbins wont run natively on Windows but we have created a virtual machine which has all of the software setup, along with the test datasets from the paper. </span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="markdown">It is based on <span class="p">[</span><span class="nv" style="color: #008080;">Bio-Linux 8</span><span class="p">](</span><span class="sx" style="color: #d14;">http://environmentalomics.org/bio-linux/</span><span class="p">)</span>. You need to first install <span class="p">[</span><span class="nv" style="color: #008080;">VirtualBox</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.virtualbox.org/</span><span class="p">)</span>, </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="markdown">then load the virtual machine, using the 'File -> Import Appliance' menu option. The root password is 'manager'.</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="markdown"><span class="p">*</span> ftp://ftp.sanger.ac.uk/pub/pathogens/pathogens-vm/pathogens-vm.latest.ova</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="markdown">More importantly though, if your trying to do bioinformatics on Windows, your not going to get very far and you should seriously consider upgrading to Linux.</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Running the tests</span></span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="markdown">The test can be run from the top level directory: </span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="markdown"></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">
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="markdown"><span class="sb" style="color: #d14;">`make check`</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Usage</span></span>
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown">To run Gubbins with default settings:</span>
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118
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown"></span>
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119
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"><span class="sb" style="color: #d14;"> run_gubbins.py [FASTA alignment]</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">@@ -73,17 +170,12 @@ Do not remove files from intermediate iterations. This option will also keep oth</td>
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="markdown">Change the model used by RAxML. The default it GTRCAT (with -V). You can set it to GTRGAMMA.</span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Generating Input files</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">======================</span></span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Generating Input files</span></span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="markdown">Any application which can generate a whole genome multi-FASTA alignment can be used with Gubbins, such as <span class="p">[</span><span class="nv" style="color: #008080;">Snippy</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/tseemann/snippy</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="markdown"> </span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Output files </span></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">==========</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="markdown"><span class="gh" style="color: #999;">Prefix</span></span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="markdown"><span class="gh" style="color: #999;">------</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Output files </span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__Prefix__</span> </span>
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<pre style="margin: 0;"> <span id="LC179" class="line" lang="markdown">If a prefix is not defined with the –prefix option, the default prefix of the output files is:</span>
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="markdown">X.Y</span>
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="markdown"></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">@@ -91,10 +183,7 @@ where:</td>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="markdown">X = Prefix taken from the input fasta file</span>
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="markdown">Y = Time stamp. NOTE: This will only be included in the output file prefix if the –u flag has been selected</span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown"></span>
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96
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="gh" style="color: #999;">Output file suffices:</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown"><span class="gh" style="color: #999;">---------------------</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="markdown"><span class="gs" style="font-weight: 600;">__Output file suffices:__</span> </span>
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="markdown"><span class="sb" style="color: #d14;"> .recombination_predictions.embl</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="markdown"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="132" 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="221" 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">@@ -132,19 +221,28 @@ Final phylogenetic tree in newick format.</td>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="markdown"><span class="sb" style="color: #d14;"> </span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="markdown">Final phylogenetic tree in newick format but with internal node labels.</span>
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<pre style="margin: 0;"> <span id="LC223" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## License</span></span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="markdown">Gubbins is free software, licensed under <span class="p">[</span><span class="nv" style="color: #008080;">GPLv2</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/blob/master/LICENSE</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Feedback/Issues</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="markdown">We currently do not have the resources to provide support for Gubbins. However, the community might be able to help you out if you report any issues about usage of the software to the <span class="p">[</span><span class="nv" style="color: #008080;">issues page</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/sanger-pathogens/gubbins/issues</span><span class="p">)</span>.</span>
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135
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<pre style="margin: 0;"> <span id="LC229" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Citation</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="markdown">If you use this software please cite:</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="markdown"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>Croucher N. J., Page A. J., Connor T. R., Delaney A. J., Keane J. A., Bentley S. D., Parkhill J., Harris S.R.</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="markdown">"Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins". doi:10.1093/nar/gku1196, Nucleic Acids Research, 2014.]</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="markdown">(http://nar.oxfordjournals.org/content/43/3/e15)</span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Further Information</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="markdown">For more information on this software see the <span class="p">[</span><span class="nv" style="color: #008080;">Gubbins webpage</span><span class="p">](</span><span class="sx" style="color: #d14;">http://sanger-pathogens.github.io/gubbins/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC138" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Data from the paper</span></span>
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<pre style="margin: 0;">-<span id="LC139" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">===================</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Data from the paper</span></span>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="markdown"><span class="p">*</span> ftp://ftp.sanger.ac.uk/pub/project/pathogens/gubbins/PMEN1.aln.gz</span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="markdown"><span class="p">*</span> ftp://ftp.sanger.ac.uk/pub/project/pathogens/gubbins/ST239.aln.gz</span>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC143" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Midpoint rerooting</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">==================</span></span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Midpoint rerooting</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="markdown">From version 1.3.5 (25/6/15) to version 1.4.6 (29/2/16) trees were not midpoint rerooted by default. This doesnt have any effect on the recombination detection, but the output trees may not look as expected. Users are advised to upgrade to the latest version.</span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">Ancestral sequence reconstruction</span></span>
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">==================</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Ancestral sequence reconstruction</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="markdown">From version 2.0.0 onwards, RAxML is used to reconstruction ancestral sequences instead of fastML. RAxML doesnt always produce results as you would expect so the results can be lower quaility than fastML. If you would like to stick with fastML for ancestral sequence reconstruction, please checkout and install v1.4.9.</span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="markdown"></span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">v2.3.2 - 12 Jan 2018</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">v2.3.4 - 30 July 2018</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">-----</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Dynamically allocate memory of arrays to circumvent segmentation faults,</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">which occur on alignments with a large number of SNPs and are due to stack overflow.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">v2.3.3 - 26 July 2018</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">Supply a Dockerfile independent from the Debian package.</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">v2.3.2 - 29 June 2018</span>
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2
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">-----</span>
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3
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<td class="diff-line-num new_line" data-linenumber="12" 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">
12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Update installation instructions to remove all reference to HomeBrew.</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Improve handling of several arguments that have a fixed set of possible values.</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Fix of test suite.</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Remove gubbins_drawer.</span>
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4
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<td class="diff-line-num new_line" data-linenumber="16" 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">
16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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5
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<td class="diff-line-num new_line" data-linenumber="17" 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">
17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">v2.3.1 - 22 Sept 2017</span>
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6
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18
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">-----</span>
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