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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/blends-team/med">Debian Blends Team / med</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/blends-team/med/-/commit/dfcf44928f3e416bebc9ac784d06267a4d2dc89c">dfcf4492</a></strong>
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<span>by Andreas Tille</span>
<i>at 2020-06-29T08:22:24+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add trf
</pre>
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<h4>1 changed file:</h4>
<ul>
<li class="file-stats">
<a href="#26b0fba1305554e48a6078ef69d0cfe948ad5765">
tasks/bio
</a>
</li>
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<h4>Changes:</h4>
<li id="26b0fba1305554e48a6078ef69d0cfe948ad5765">
<a href="https://salsa.debian.org/blends-team/med/-/commit/dfcf44928f3e416bebc9ac784d06267a4d2dc89c#26b0fba1305554e48a6078ef69d0cfe948ad5765"><strong>tasks/bio</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1394" 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">@@ -1394,6 +1394,8 @@ X-Recommends: treevolve</td>
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<td class="diff-line-num old_line" data-linenumber="1394" 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">
1394
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<td class="diff-line-num new_line" data-linenumber="1394" 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">
1394
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<pre style="margin: 0;"> <span id="LC1394" class="line" lang="mosel"><span class="n" style="color: #333;">X</span><span class="p">-</span><span class="n" style="color: #333;">Comment</span><span class="p">:</span> <span class="n" style="color: #333;">Homepage</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">software</span> <span class="n" style="color: #333;">vanished</span><span class="p">,</span> <span class="n" style="color: #333;">packaging</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">SVN</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">obviosely</span> <span class="n" style="color: #333;">stalled</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1395" 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">
1395
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<td class="diff-line-num new_line" data-linenumber="1395" 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">
1395
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<pre style="margin: 0;"> <span id="LC1395" class="line" lang="mosel"> <span class="n" style="color: #333;">Feel</span> <span class="n" style="color: #333;">free</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">delete</span> <span class="n" style="color: #333;">the</span> <span class="s1" style="color: #d14;">'X-'</span> <span class="k" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">front</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">you</span> <span class="n" style="color: #333;">intend</span> <span class="k" style="font-weight: 600;">to</span> <span class="k" style="font-weight: 600;">do</span> <span class="n" style="color: #333;">something</span> <span class="n" style="color: #333;">on</span> <span class="n" style="color: #333;">this</span> <span class="k" style="font-weight: 600;">package</span></span>
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<td class="diff-line-num old_line" data-linenumber="1396" 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">
1396
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<td class="diff-line-num new_line" data-linenumber="1396" 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">
1396
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<pre style="margin: 0;"> <span id="LC1396" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="1397" style="width: 35px; color: rgba(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="1397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1397
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<pre style="margin: 0;">+<span id="LC1397" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">trf</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1397" style="width: 35px; color: rgba(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="1398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1398
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<pre style="margin: 0;">+<span id="LC1398" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1397" 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">
1397
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<td class="diff-line-num new_line" data-linenumber="1399" 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">
1399
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<pre style="margin: 0;"> <span id="LC1399" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">trinityrnaseq</span></span>
</pre>
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1398
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<td class="diff-line-num new_line" data-linenumber="1400" 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">
1400
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<pre style="margin: 0;"> <span id="LC1400" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1399" 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">
1399
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<td class="diff-line-num new_line" data-linenumber="1401" 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">
1401
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<pre style="margin: 0;"> <span id="LC1401" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">uc</span><span class="p">-</span><span class="n" style="color: #333;">echo</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="2684" 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="2686" 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">@@ -2684,20 +2686,6 @@ Pkg-Description: annotate genomes and create genome databases</td>
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2684
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<td class="diff-line-num new_line" data-linenumber="2686" 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">
2686
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2686" class="line" lang="mosel"><span class="s1" style="color: #d14;"> especially useful for emerging model organism projects with minimal</span></span>
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<td class="diff-line-num old_line" data-linenumber="2685" 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">
2685
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<td class="diff-line-num new_line" data-linenumber="2687" 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">
2687
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2687" class="line" lang="mosel"><span class="s1" style="color: #d14;"> bioinformatics expertise and computer resources</span></span>
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<td class="diff-line-num old_line" data-linenumber="2686" 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">
2686
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<td class="diff-line-num new_line" data-linenumber="2688" 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">
2688
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<pre style="margin: 0;"> <span id="LC2688" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="2687" 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">
2687
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2687" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: rmblast</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2688" 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">
2688
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2688" class="line" lang="mosel"><span class="s1" style="color: #d14;">Homepage: http://tandem.bu.edu/trf/trf.html</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2689" 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">
2689
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2689" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: Same as blast2</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2690" 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">
2690
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2690" class="line" lang="mosel"><span class="s1" style="color: #d14;">Pkg-Description: RepeatMasker compatible version of the standard NCBI BLAST</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2691" 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">
2691
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2691" class="line" lang="mosel"><span class="s1" style="color: #d14;"> RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2692" 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">
2692
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2692" class="line" lang="mosel"><span class="s1" style="color: #d14;"> suite. The primary difference between this distribution and the NCBI</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2693" 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">
2693
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2693" class="line" lang="mosel"><span class="s1" style="color: #d14;"> distribution is the addition of a new program "rmblastn" for use with</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2694" 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">
2694
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2694" class="line" lang="mosel"><span class="s1" style="color: #d14;"> RepeatMasker and RepeatModeler.</span></span>
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2695
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2695" class="line" lang="mosel"><span class="s1" style="color: #d14;"> RMBlast supports RepeatMasker searches by adding a few necessary features</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2696" 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">
2696
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2696" class="line" lang="mosel"><span class="s1" style="color: #d14;"> to the stock NCBI blastn program. These include: Support for custom matrices</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2697" 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">
2697
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2697" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ( without KA-Statistics ). Support for cross_match-like complexity adjusted</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2698" 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">
2698
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2698" class="line" lang="mosel"><span class="s1" style="color: #d14;"> scoring. Cross_match is Phil Green'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">seeded</span> <span class="n" style="color: #333;">smith</span><span class="p">-</span><span class="n" style="color: #333;">waterman</span> <span class="n" style="color: #333;">search</span> <span class="n" style="color: #333;">algorithm</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2699" 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">
2699
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2699" class="line" lang="mosel"> <span class="n" style="color: #333;">Support</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">cross_match</span><span class="p">-</span><span class="n" style="color: #333;">like</span> <span class="n" style="color: #333;">masklevel</span> <span class="n" style="color: #333;">filtering</span><span class="p">.</span></span>
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<td class="diff-line-num old old_line" data-linenumber="2700" 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">
2700
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<td class="diff-line-num new_line old" data-linenumber="2689" 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="LC2700" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="2701" 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">
2701
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<td class="diff-line-num new_line" data-linenumber="2689" 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">
2689
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<pre style="margin: 0;"> <span id="LC2689" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: e-hive</span></span>
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<td class="diff-line-num old_line" data-linenumber="2702" 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">
2702
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<td class="diff-line-num new_line" data-linenumber="2690" 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">
2690
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<pre style="margin: 0;"> <span id="LC2690" class="line" lang="mosel"><span class="s1" style="color: #d14;">Homepage: http://www.ensembl.org/info/docs/eHive/index.html</span></span>
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<td class="diff-line-num old_line" data-linenumber="2703" 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">
2703
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<td class="diff-line-num new_line" data-linenumber="2691" 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">
2691
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<pre style="margin: 0;"> <span id="LC2691" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: Not specified</span></span>
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