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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/c80e5cf29453a3e76ff0909dfb1a106b37f249ce">c80e5cf2</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-26T09:54:50Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">tracerunner now in Git
</pre>
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<h4>1 changed file:</h4>
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<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/c80e5cf29453a3e76ff0909dfb1a106b37f249ce#26b0fba1305554e48a6078ef69d0cfe948ad5765"><strong>tasks/bio</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1085" 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">@@ -1085,6 +1085,8 @@ Recommends: tn-seqexplorer</td>
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1085
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<td class="diff-line-num new_line" data-linenumber="1085" 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">
1085
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<pre style="margin: 0;"> <span id="LC1085" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="1086" 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">
1086
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<td class="diff-line-num new_line" data-linenumber="1086" 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">
1086
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<pre style="margin: 0;"> <span id="LC1086" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">toil</span></span>
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<td class="diff-line-num old_line" data-linenumber="1087" 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">
1087
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<td class="diff-line-num new_line" data-linenumber="1087" 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">
1087
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<pre style="margin: 0;"> <span id="LC1087" class="line" lang="mosel"></span>
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<td class="diff-line-num new new_line" data-linenumber="1088" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1088
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<pre style="margin: 0;">+<span id="LC1088" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">tracetuner</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1088" style="width: 35px; color: rgba(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="1089" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1089
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1089" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="1088" 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">
1088
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<td class="diff-line-num new_line" data-linenumber="1090" 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">
1090
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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="LC1090" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">transrate</span><span class="p">-</span><span class="n" style="color: #333;">tools</span></span>
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1089
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<td class="diff-line-num new_line" data-linenumber="1091" 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">
1091
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<pre style="margin: 0;"> <span id="LC1091" class="line" lang="mosel"></span>
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1090
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<td class="diff-line-num new_line" data-linenumber="1092" 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">
1092
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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="LC1092" class="line" lang="mosel"><span class="n" style="color: #333;">Recommends</span><span class="p">:</span> <span class="n" style="color: #333;">treeview</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="1289" 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">@@ -1287,35 +1289,6 @@ Pkg-Description: draw phylogenetic trees</td>
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1287
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<td class="diff-line-num new_line" data-linenumber="1289" 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">
1289
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<pre style="margin: 0;"> <span id="LC1289" class="line" lang="mosel"><span class="s1" style="color: #d14;"> PhpPhylotree is a web application that is able to draw phylogenetic trees.</span></span>
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<td class="diff-line-num old_line" data-linenumber="1288" 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">
1288
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<td class="diff-line-num new_line" data-linenumber="1290" 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">
1290
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="mosel"><span class="s1" style="color: #d14;"> It produces an SVG (Scalable Vector Graphic) file from phylip/newick tree files.</span></span>
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1289
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<td class="diff-line-num new_line" data-linenumber="1291" 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">
1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="mosel"></span>
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1290
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<td class="diff-line-num new_line old" data-linenumber="1292" 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="LC1290" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: tracetuner</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1291" 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">
1291
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<td class="diff-line-num new_line old" data-linenumber="1292" 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="LC1291" class="line" lang="mosel"><span class="s1" style="color: #d14;">Homepage: https://sourceforge.net/p/tracetuner</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1292" 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">
1292
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<td class="diff-line-num new_line old" data-linenumber="1292" 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="LC1292" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: GPL; but US Patent #6,681,186</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1293" 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">
1293
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<td class="diff-line-num new_line old" data-linenumber="1292" 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="LC1293" class="line" lang="mosel"><span class="s1" style="color: #d14;">Pkg-Description: DNA sequencing and trace processing</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1294" 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">
1294
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<td class="diff-line-num new_line old" data-linenumber="1292" 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="LC1294" class="line" lang="mosel"><span class="s1" style="color: #d14;"> TraceTuner is a DNA sequencing quality value, base calling and trace</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1295" 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">
1295
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<td class="diff-line-num new_line old" data-linenumber="1292" 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="LC1295" class="line" lang="mosel"><span class="s1" style="color: #d14;"> processing software application originally developed by Paracel,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1296" 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">
1296
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<pre style="margin: 0;">-<span id="LC1296" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Inc. While providing a flexible interface and capability to adopt the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1297" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
1297
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<pre style="margin: 0;">-<span id="LC1297" class="line" lang="mosel"><span class="s1" style="color: #d14;"> "pure" base calls produced by Phred, KB or any other "original"</span></span>
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1298
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<pre style="margin: 0;">-<span id="LC1298" class="line" lang="mosel"><span class="s1" style="color: #d14;"> caller, it offers competitive features not currently available in</span></span>
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1299
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<pre style="margin: 0;">-<span id="LC1299" class="line" lang="mosel"><span class="s1" style="color: #d14;"> other tools, such as customized calibration of quality values,</span></span>
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1300
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<pre style="margin: 0;">-<span id="LC1300" class="line" lang="mosel"><span class="s1" style="color: #d14;"> advanced heterozygote and mixed base calling and deconvolving the</span></span>
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1301
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<pre style="margin: 0;">-<span id="LC1301" class="line" lang="mosel"><span class="s1" style="color: #d14;"> "mixed" electropherograms resulting from the presence of indels into</span></span>
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1302
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<pre style="margin: 0;">-<span id="LC1302" class="line" lang="mosel"><span class="s1" style="color: #d14;"> a couple of "pure" electropherograms. Previous versions of TraceTuner</span></span>
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1303
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<pre style="margin: 0;">-<span id="LC1303" class="line" lang="mosel"><span class="s1" style="color: #d14;"> were used by Celera Genomics to process over 27 million reads from</span></span>
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1304
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<pre style="margin: 0;">-<span id="LC1304" class="line" lang="mosel"><span class="s1" style="color: #d14;"> both Drosophila and human genome projects and by Applied Biosystems,</span></span>
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1305
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<pre style="margin: 0;">-<span id="LC1305" class="line" lang="mosel"><span class="s1" style="color: #d14;"> as a component of its SNP detection and genotyping software product</span></span>
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1306
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<pre style="margin: 0;">-<span id="LC1306" class="line" lang="mosel"><span class="s1" style="color: #d14;"> SeqScape. TraceTuner implements an advanced peak processing</span></span>
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1307
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<pre style="margin: 0;">-<span id="LC1307" class="line" lang="mosel"><span class="s1" style="color: #d14;"> technology for resolving overlapping peaks of the same dye color into</span></span>
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1308
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<pre style="margin: 0;">-<span id="LC1308" class="line" lang="mosel"><span class="s1" style="color: #d14;"> individual, or "intrinsic" peaks. This technology was protected by US</span></span>
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1309
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<pre style="margin: 0;">-<span id="LC1309" class="line" lang="mosel"><span class="s1" style="color: #d14;"> Patent #6,681,186. Currently, TraceTuner is an open source software,</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1310" 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">
1310
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<pre style="margin: 0;">-<span id="LC1310" class="line" lang="mosel"><span class="s1" style="color: #d14;"> which has been used by J. Craig Venter Institute'</span><span class="n" style="color: #333;">s</span> <span class="n" style="color: #333;">DNA</span> <span class="n" style="color: #333;">Sequencing</span> <span class="k" style="font-weight: 600;">and</span></span>
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1311
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<pre style="margin: 0;">-<span id="LC1311" class="line" lang="mosel"> <span class="n" style="color: #333;">Resequencing</span> <span class="n" style="color: #333;">pipelines</span><span class="p">.</span></span>
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1312
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<pre style="margin: 0;">-<span id="LC1312" class="line" lang="mosel"> <span class="p">.</span></span>
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1313
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<td class="diff-line-num new_line old" data-linenumber="1292" 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="LC1313" class="line" lang="mosel"> <span class="n" style="color: #333;">The</span> <span class="n" style="color: #333;">TraceTuner</span> <span class="n" style="color: #333;">Software</span> <span class="p">(</span><span class="n" style="color: #333;">Copyright</span> <span class="m" style="color: #099;">1999</span><span class="p">-</span><span class="m" style="color: #099;">2003</span><span class="p">,</span> <span class="n" style="color: #333;">Paracel</span><span class="p">,</span> <span class="n" style="color: #333;">Inc</span><span class="p">.</span> <span class="n" style="color: #333;">All</span></span>
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1314
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<pre style="margin: 0;">-<span id="LC1314" class="line" lang="mosel"> <span class="n" style="color: #333;">rights</span> <span class="n" style="color: #333;">reserved</span><span class="p">.)</span> <span class="p">(</span><span class="n" style="color: #333;">the</span> <span class="s2" style="color: #d14;">"Software"</span><span class="p">)</span> <span class="n" style="color: #333;">is</span> <span class="n" style="color: #333;">covered</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">US</span> <span class="n" style="color: #333;">Patent</span> <span class="p">#</span><span class="m" style="color: #099;">6</span><span class="p">,</span><span class="m" style="color: #099;">681</span><span class="p">,</span><span class="m" style="color: #099;">186</span> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">is</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1315" 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">
1315
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<td class="diff-line-num new_line old" data-linenumber="1292" 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="LC1315" class="line" lang="mosel"> <span class="n" style="color: #333;">being</span> <span class="n" style="color: #333;">made</span> <span class="n" style="color: #333;">available</span> <span class="n" style="color: #333;">free</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">charge</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">Applera</span> <span class="n" style="color: #333;">Corporation</span> <span class="n" style="color: #333;">subject</span> <span class="k" style="font-weight: 600;">to</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">terms</span></span>
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1316
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<pre style="margin: 0;">-<span id="LC1316" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">conditions</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">the</span> <span class="n" style="color: #333;">GNU</span> <span class="n" style="color: #333;">General</span> <span class="k" style="font-weight: 600;">Public</span> <span class="n" style="color: #333;">License</span><span class="p">,</span> <span class="k" style="font-weight: 600;">version</span> <span class="m" style="color: #099;">2</span><span class="p">,</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">published</span> <span class="n" style="color: #333;">by</span> <span class="n" style="color: #333;">the</span></span>
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<td class="diff-line-num old old_line" data-linenumber="1317" 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">
1317
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<pre style="margin: 0;">-<span id="LC1317" class="line" lang="mosel"> <span class="n" style="color: #333;">Free</span> <span class="n" style="color: #333;">Software</span> <span class="n" style="color: #333;">Foundation</span> <span class="p">(</span><span class="n" style="color: #333;">the</span> <span class="s2" style="color: #d14;">"GNU General Public License"</span><span class="p">).</span></span>
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1318
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<pre style="margin: 0;">-<span id="LC1318" class="line" lang="mosel"></span>
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<td class="diff-line-num old_line" data-linenumber="1319" 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">
1319
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1292
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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="mosel"><span class="s1" style="color: #d14;">Recommends: twain</span></span>
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1320
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1293
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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="LC1293" class="line" lang="mosel"><span class="s1" style="color: #d14;">Homepage: http://cbcb.umd.edu/software/pirate/twain/twain.shtml</span></span>
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<pre style="margin: 0;"> <span id="LC1294" class="line" lang="mosel"><span class="s1" style="color: #d14;">License: Open Source</span></span>
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