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<h3>
Jelmer Vernooij pushed to branch master
at <a href="https://salsa.debian.org/med-team/clustalw">Debian Med / clustalw</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/clustalw/commit/184712edd521cbb4787178803250a25bebcc526c">184712ed</a></strong>
<div>
<span>by Jelmer Vernooij</span>
<i>at 2018-10-20T13:51:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Use secure copyright file specification URI.
Fixes lintian: insecure-copyright-format-uri
See https://lintian.debian.org/tags/insecure-copyright-format-uri.html for more details.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/clustalw/commit/18f08151307deb51d1356ef9a9e4f4f3856c9c16">18f08151</a></strong>
<div>
<span>by Jelmer Vernooij</span>
<i>at 2018-10-20T13:51:34Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
</pre>
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<h4>3 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/clustalw/compare/ac6a66cc81907fb5c0eed5f6d4959ead79877b6d...18f08151307deb51d1356ef9a9e4f4f3856c9c16#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">clustalw (2.1+lgpl-7) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Use secure copyright file specification URI.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * Trim trailing whitespace.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> -- Jelmer Vernooij <jelmer@debian.org> Sat, 20 Oct 2018 13:51:34 +0000</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">clustalw (2.1+lgpl-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> * debhelper 11</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="120" 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="127" 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">@@ -120,7 +127,7 @@ clustalw (2.0.9-1) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="plaintext"> and therefore removed here.</span>
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="plaintext"> * debian/copyright: added a disclaimer clarifying that this package is not</span>
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext"> part of the Debian operating system (requirement of Policy 3.8.0).</span>
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<pre style="margin: 0;">-<span id="LC123" class="line" lang="plaintext"> * debian/control:<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext"> * debian/control:</span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="plaintext"> - Updated Standards-Version to 3.8.0.</span>
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<td class="diff-line-num old_line" data-linenumber="125" 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="LC132" class="line" lang="plaintext"> - Enhances: emboss (EMBOSS has a wrapper for clustalw, `emma'.)</span>
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<td class="diff-line-num old_line" data-linenumber="126" 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="LC133" class="line" lang="plaintext"> * debian/clustaw.1*: incremented version number.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="152" 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="159" 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">@@ -152,7 +159,7 @@ clustalw (2.0.7-1) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC159" class="line" lang="plaintext"> getSeqRange routines.</span>
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"> - Fixes bug 119: build with g++ 4.3.</span>
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="plaintext"> * Removed debian/patches/bug_119_gpp4.3-autoptr.patch, obsoleted by the</span>
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155
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<pre style="margin: 0;">-<span id="LC155" class="line" lang="plaintext"> above correction.<span class="idiff left right"> </span></span>
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<td class="diff-line-num new old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext"> above correction.</span>
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156
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163
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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext"> * Incremented version number in debian/clustalw.1*</span>
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<td class="diff-line-num old_line" data-linenumber="157" 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">
157
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164
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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext"> * Uptated debian/copyright to the latest draft of the format.</span>
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<td class="diff-line-num old_line" data-linenumber="158" 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">
158
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165
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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="199" 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="206" 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">@@ -199,7 +206,7 @@ clustalw (2.0.4-1) unstable; urgency=low</td>
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<td class="diff-line-num old_line" data-linenumber="199" 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">
199
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206
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext"> - fixed bug where Pseudo -FASTA format files were not being processed</span>
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<td class="diff-line-num old_line" data-linenumber="200" 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">
200
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<td class="diff-line-num new_line" data-linenumber="207" 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="LC207" class="line" lang="plaintext"> as previously in v1.83 (v. 2.0.3)</span>
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<td class="diff-line-num old_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="plaintext"> - fixed other bugs to behave more like 1.83, and introduced a new</span>
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202
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<pre style="margin: 0;">-<span id="LC202" class="line" lang="plaintext"> '-fullhelp' option. (v 2.0.4)<span class="idiff left right"> </span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext"> '-fullhelp' option. (v 2.0.4)</span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext"> * updated debian/watch</span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext"> * moved clustalw.1 into debian folder (easier to work</span>
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="plaintext"> with svn-buildpackage)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="278" 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">@@ -271,7 +278,7 @@ clustalw (1.83-1.2) unstable; urgency=high</td>
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<td class="diff-line-num old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="plaintext"> -- Fabio Tranchitella <kobold@debian.org> Fri, 10 Nov 2006 09:16:45 +0100</span>
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC274" class="line" lang="plaintext">clustalw (1.83-1.1) unstable; urgency=low<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">clustalw (1.83-1.1) unstable; urgency=low</span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="plaintext"> * Non-maintainer upload.</span>
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<td class="diff-line-num old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="plaintext"> * lesstif1 is deprecated, transition to lesstif2 (Closes: #374241)</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="342" 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="349" 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">@@ -342,7 +349,7 @@ clustalw (1.7-9) unstable; urgency=low</td>
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="plaintext">clustalw (1.7-8) unstable; urgency=low</span>
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344
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC345" class="line" lang="plaintext"> * Adopted by new maintainer; closes: #92790<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext"> * Adopted by new maintainer; closes: #92790</span>
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346
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="plaintext"> * Updated to latest standards version and added Build-Depends (changed</span>
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354
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="plaintext"> makefile, control, dirs, docs, and rules); closes: #91132, #91411</span>
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348
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="plaintext"> * Deleted empty README.Debian file.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="374" 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="381" 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">@@ -374,7 +381,7 @@ clustalw (1.7-5) unstable; urgency=low</td>
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374
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="plaintext"></span>
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375
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="plaintext">clustalw (1.7-4) unstable; urgency=low</span>
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376
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<pre style="margin: 0;"> <span id="LC383" class="line" lang="plaintext"></span>
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377
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<pre style="margin: 0;">-<span id="LC377" class="line" lang="plaintext"> * Compiles with -mieee on the Alpha: otherwise, floating exception since<span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext"> * Compiles with -mieee on the Alpha: otherwise, floating exception since</span>
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378
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="plaintext"> ClustalW divides by zero (yuck!)</span>
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379
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC387" class="line" lang="plaintext"> -- Stephane Bortzmeyer <bortzmeyer@debian.org> Wed, 2 Dec 1998 16:16:02 +0100</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="389" 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">@@ -382,7 +389,7 @@ clustalw (1.7-4) unstable; urgency=low</td>
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382
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389
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<pre style="margin: 0;"> <span id="LC389" class="line" lang="plaintext">clustalw (1.7-3) unstable; urgency=low</span>
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383
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390
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<pre style="margin: 0;"> <span id="LC390" class="line" lang="plaintext"></span>
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384
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<pre style="margin: 0;"> <span id="LC391" class="line" lang="plaintext"> * Tests and samples added</span>
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385
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<pre style="margin: 0;">-<span id="LC385" class="line" lang="plaintext"> * On line help file added<span class="idiff left right"> </span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="plaintext"> * On line help file added</span>
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386
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<pre style="margin: 0;"> <span id="LC393" class="line" lang="plaintext"></span>
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387
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394
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<pre style="margin: 0;"> <span id="LC394" class="line" lang="plaintext"> -- Stephane Bortzmeyer <bortzmeyer@debian.org> Tue, 1 Dec 1998 15:57:50 +0100</span>
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388
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395
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<pre style="margin: 0;"> <span id="LC395" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/clustalw/compare/ac6a66cc81907fb5c0eed5f6d4959ead79877b6d...18f08151307deb51d1356ef9a9e4f4f3856c9c16#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,4 +30,4 @@ Description: global multiple nucleotide or peptide sequence alignment</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> The output of Clustal W can be edited manually but preferably with an</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> alignment editor like SeaView or within its companion Clustal X. When building</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> a model from your alignment, this can be applied for improved database</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> searches. The Debian package hmmer creates such in form of an HMM.<span class="idiff left right"> </span></span></pre>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> searches. The Debian package hmmer creates such in form of an HMM.</span></pre>
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<a href="https://salsa.debian.org/med-team/clustalw/compare/ac6a66cc81907fb5c0eed5f6d4959ead79877b6d...18f08151307deb51d1356ef9a9e4f4f3856c9c16#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: http<span class="idiff left right">s</span>://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Upstream-Name: ClustalQ</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Source: http://www.clustal.org/download/current/clustalw-2.1.tar.gz</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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