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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/blends-team/med">Debian Blends Team / med</a>
</h3>
<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/blends-team/med/commit/55132eadd15636faad18298453f8f96c454bd552">55132ead</a></strong>
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<span>by Steffen Möller</span>
<i>at 2018-09-05T12:11:09Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">ELPH is now in distribution
Also Updated upstream URL of Lucy.</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#26b0fba1305554e48a6078ef69d0cfe948ad5765">
tasks/bio
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<h4>Changes:</h4>
<li id="26b0fba1305554e48a6078ef69d0cfe948ad5765">
<a href="https://salsa.debian.org/blends-team/med/commit/55132eadd15636faad18298453f8f96c454bd552#26b0fba1305554e48a6078ef69d0cfe948ad5765"><strong>tasks/bio</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="78" 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">@@ -78,6 +78,8 @@ Recommends: ghmm, hmmer</td>
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78
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78
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="mosel"></span>
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79
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">exonerate</span></span>
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80
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80
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC80" class="line" lang="mosel"></span>
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<td class="diff-line-num new old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">elph</span></span>
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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="81" 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">
81
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<td class="diff-line-num new_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">dialign</span></span>
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82
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84
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="mosel"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="83" 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">
83
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<td class="diff-line-num new_line" data-linenumber="85" 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">
85
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC85" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">dialign</span><span class="p">-</span><span class="n" style="color: #333;">tx</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1690" 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="1692" 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">@@ -1690,24 +1692,6 @@ Pkg-Description: The microRNA sequence database</td>
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1690
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<td class="diff-line-num new_line" data-linenumber="1692" 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">
1692
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<pre style="margin: 0;"> <span id="LC1692" class="line" lang="mosel"><span class="s1" style="color: #d14;"> It is possible that mirbase will not be a package from the main archive, but</span></span>
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<td class="diff-line-num old_line" data-linenumber="1691" 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">
1691
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<td class="diff-line-num new_line" data-linenumber="1693" 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">
1693
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC1693" class="line" lang="mosel"><span class="s1" style="color: #d14;"> will be autogenerated as part of a larger data packaging effort.</span></span>
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1692
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<td class="diff-line-num new_line" data-linenumber="1694" 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">
1694
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<pre style="margin: 0;"> <span id="LC1694" class="line" lang="mosel"></span>
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<td class="diff-line-num old old_line" data-linenumber="1693" 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">
1693
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<td class="diff-line-num new_line old" data-linenumber="1695" 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="LC1693" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: elph</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1694" 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">
1694
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<td class="diff-line-num new_line old" data-linenumber="1695" 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="LC1694" class="line" lang="mosel"><span class="s1" style="color: #d14;">Homepage: http://www.cbcb.umd.edu/software/ELPH/</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1695" 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">
1695
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<td class="diff-line-num new_line old" data-linenumber="1695" 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="LC1695" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: Artistic</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1696" 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">
1696
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<td class="diff-line-num new_line old" data-linenumber="1695" 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="LC1696" class="line" lang="mosel"><span class="s1" style="color: #d14;">Pkg-Description: motif finder that can find ribosome binding sites, exon splicing enhancers, or regulatory sites</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1697" 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">
1697
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<td class="diff-line-num new_line old" data-linenumber="1695" 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="LC1697" class="line" lang="mosel"><span class="s1" style="color: #d14;"> ELPH (Estimated Locations of Pattern Hits) is a general-purpose Gibbs</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1698" 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">
1698
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<pre style="margin: 0;">-<span id="LC1698" class="line" lang="mosel"><span class="s1" style="color: #d14;"> sampler for finding motifs in a set of DNA or protein sequences. The</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1699" 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">
1699
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<pre style="margin: 0;">-<span id="LC1699" class="line" lang="mosel"><span class="s1" style="color: #d14;"> program takes as input a set containing anywhere from a few dozen to</span></span>
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1700
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<pre style="margin: 0;">-<span id="LC1700" class="line" lang="mosel"><span class="s1" style="color: #d14;"> thousands of sequences, and searches through them for the most common</span></span>
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1701
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<pre style="margin: 0;">-<span id="LC1701" class="line" lang="mosel"><span class="s1" style="color: #d14;"> motif, assuming that each sequence contains one copy of the motif. We</span></span>
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1702
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<pre style="margin: 0;">-<span id="LC1702" class="line" lang="mosel"><span class="s1" style="color: #d14;"> have used ELPH to find patterns such as ribosome binding sites (RBSs)</span></span>
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1703
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<pre style="margin: 0;">-<span id="LC1703" class="line" lang="mosel"><span class="s1" style="color: #d14;"> and exon splicing enhancers (ESEs). See below for instructions on</span></span>
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1704
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<pre style="margin: 0;">-<span id="LC1704" class="line" lang="mosel"><span class="s1" style="color: #d14;"> downloading the complete system, including source code.</span></span>
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1705
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<pre style="margin: 0;">-<span id="LC1705" class="line" lang="mosel"><span class="s1" style="color: #d14;"> .</span></span>
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1706
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<pre style="margin: 0;">-<span id="LC1706" class="line" lang="mosel"><span class="s1" style="color: #d14;"> An online tool that uses ELPH output for identifying exon splicing</span></span>
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1707
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<pre style="margin: 0;">-<span id="LC1707" class="line" lang="mosel"><span class="s1" style="color: #d14;"> enhancers can be found at</span></span>
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1708
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<pre style="margin: 0;">-<span id="LC1708" class="line" lang="mosel"><span class="s1" style="color: #d14;"> http://www.cbcb.umd.edu/software/SeeEse/index.html .</span></span>
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1709
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<pre style="margin: 0;">-<span id="LC1709" class="line" lang="mosel"><span class="s1" style="color: #d14;">Remark: Other sequence analysis tools (http://www.cbcb.umd.edu/software/)</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1710" 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">
1710
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<pre style="margin: 0;">-<span id="LC1710" class="line" lang="mosel"></span>
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1711
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1695
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<pre style="margin: 0;"> <span id="LC1695" class="line" lang="mosel"><span class="s1" style="color: #d14;">X-Recommends: repeatfinder</span></span>
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1712
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<td class="diff-line-num new_line" data-linenumber="1696" 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">
1696
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<pre style="margin: 0;"> <span id="LC1696" class="line" lang="mosel"><span class="s1" style="color: #d14;">X-Homepage: http://www.cbcb.umd.edu/software/RepeatFinder/</span></span>
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1713
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<td class="diff-line-num new_line" data-linenumber="1697" 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">
1697
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<pre style="margin: 0;"> <span id="LC1697" class="line" lang="mosel"><span class="s1" style="color: #d14;">X-License: Artistic</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1951" 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="1935" 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">@@ -1951,7 +1935,7 @@ Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html.</td>
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1951
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1935
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<pre style="margin: 0;"> <span id="LC1935" class="line" lang="mosel"> <span class="n" style="color: #333;">redistribution</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">their</span> <span class="n" style="color: #333;">software</span><span class="p">.</span> <span class="n" style="color: #333;">Someone</span> <span class="n" style="color: #333;">please</span> <span class="n" style="color: #333;">go</span> <span class="n" style="color: #333;">for</span> <span class="n" style="color: #333;">it</span><span class="p">.</span></span>
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<td class="diff-line-num old_line" data-linenumber="1952" 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">
1952
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<td class="diff-line-num new_line" data-linenumber="1936" 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">
1936
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<pre style="margin: 0;"> <span id="LC1936" class="line" lang="mosel"></span>
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1953
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<td class="diff-line-num new_line" data-linenumber="1937" 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">
1937
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<pre style="margin: 0;"> <span id="LC1937" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">lucy</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1954" 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">
1954
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<td class="diff-line-num new_line old" data-linenumber="1938" 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="LC1954" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;"><span class="idiff left">rcc</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">uga</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">edu</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">applications</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">bioinformatics</span></span><span class="p"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">lucy</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">html</span></span></span>
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<td class="diff-line-num new old_line" data-linenumber="1955" style="width: 35px; color: rgba(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="1938" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1938
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<pre style="margin: 0;">+<span id="LC1938" class="line" lang="mosel"><span class="n" style="color: #333;">Homepage</span><span class="p">:</span> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;"><span class="idiff left">lucy</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">sourceforge</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">net</span></span><span class="p"><span class="idiff right">/</span></span></span>
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1955
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<td class="diff-line-num new_line" data-linenumber="1939" 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">
1939
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<pre style="margin: 0;"> <span id="LC1939" class="line" lang="mosel"><span class="n" style="color: #333;">License</span><span class="p">:</span> <span class="n" style="color: #333;">GPL</span></span>
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<td class="diff-line-num old_line" data-linenumber="1956" 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">
1956
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<td class="diff-line-num new_line" data-linenumber="1940" 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">
1940
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<pre style="margin: 0;"> <span id="LC1940" class="line" lang="mosel"><span class="n" style="color: #333;">Responsible</span><span class="p">:</span> <span class="n" style="color: #333;">BioLinux</span> <span class="p">-</span> <span class="n" style="color: #333;">Dan</span> <span class="n" style="color: #333;">Swan</span> <span class="p"><</span><span class="n" style="color: #333;">dswan</span><span class="p">@</span><span class="n" style="color: #333;">ceh</span><span class="p">.</span><span class="n" style="color: #333;">ac</span><span class="p">.</span><span class="n" style="color: #333;">uk</span><span class="p">></span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="1957" 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">
1957
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<td class="diff-line-num new_line" data-linenumber="1941" 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">
1941
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<pre style="margin: 0;"> <span id="LC1941" class="line" lang="mosel"><span class="n" style="color: #333;">Pkg</span><span class="p">-</span><span class="n" style="color: #333;">URL</span><span class="p">:</span> <span class="n" style="color: #333;">http</span><span class="p">://</span><span class="n" style="color: #333;">nebc</span><span class="p">.</span><span class="n" style="color: #333;">nox</span><span class="p">.</span><span class="n" style="color: #333;">ac</span><span class="p">.</span><span class="n" style="color: #333;">uk</span><span class="p">/</span><span class="n" style="color: #333;">bio</span><span class="p">-</span><span class="n" style="color: #333;">linux</span><span class="p">/</span><span class="n" style="color: #333;">dists</span><span class="p">/</span><span class="n" style="color: #333;">unstable</span><span class="p">/</span><span class="n" style="color: #333;">bio</span><span class="p">-</span><span class="n" style="color: #333;">linux</span><span class="p">/</span><span class="n" style="color: #333;">binary</span><span class="p">-</span><span class="n" style="color: #333;">i386</span><span class="p">/</span></span>
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