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Manual changes for 1.11
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@DMaddison
DMaddison committed Aug 29, 2014
2 parents b4937dc + 93f932f commit f4d1790
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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/Templates/ChromaseqTemplate.dwt
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<td width="33%" align="right"><div id="subtitle"><!-- TemplateBeginEditable name="subtitle" -->subtitle<!-- TemplateEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/acknowledgements.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Acknowledgements<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Processing Additional Chromatograms<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/callingBases.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Calling Bases <!-- InstanceEndEditable --></div></td>
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<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Chromaseq E-mail List<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/chromatograms.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Preparing Chromatograms<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/citation.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Citation<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/conflicts.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Detecting Conflicts<!-- InstanceEndEditable --></div></td>
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<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/display.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Other Display Options <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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17 changes: 10 additions & 7 deletions Source/mesquite/chromaseq/aChromaseqIntro/manual/download.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Download<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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<p>You can download and install Chromaseq in one of two ways:</p>
<ol>
<li>Start <strong>Mesquite 3.0</strong> or later. Choose File&gt;Check Now for Notices/Installs. In the dialog box that is presented, enter <strong>http://mesquiteproject.org/packages/chromaseq/install.xml</strong>, and press OK.</li>
<li>Download the package from this page by clicking on the link below, unzip the file downloaded, and move the <strong>chromaseq</strong> directory into your Mesquite_Folder/mesquite/ directory. </li>
<li>Download the package from this page from the Chromaseq Github <a href="https://github.com/MesquiteProject/Chromaseq/releases">release page</a>, and download the latest release by pressing the appropriate green button. We suggest you download the <strong>zip</strong> version if you have MacOSX or Windows, and the <strong>tgz</strong> version if you have a Linux system. To install Cartographer, open up the
downloaded file, find the directory contained therein
called &quot;chromaseq&quot;,
and move that into the &quot;mesquite&quot; directory of your
installed &quot;Mesquite_Folder&quot;
directory.
If you wish, you could instead move it into <a href="http://mesquiteproject.org/Mesquite_Folder/docs/mesquite/modules.html#places">other
locations supported by Mesquite</a>. </p>
</li>
</ol>
<h3>Download</h3>
<ul>
<li><a href="https://github.com/MesquiteProject/Chromaseq/releases/download/1.1/Chromaseq.1.1.zip">zip file (MacOS, Windows)</a></li>
<li><a href="https://github.com/MesquiteProject/Chromaseq/releases/download/1.1/Chromaseq.1.1.tar.gz">tar.gz (UNIX/Linux)</a></li>
</ul>
<p><font >If you previously downloaded either the base system
of Mesquite or Chromaseq, and intend to download a new version of Mesquite,
you
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Multiple Reads/Contigs at Once<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/faq.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Frequently Asked Questions <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->File Naming Rules<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/future.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Future Directions <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/genbank.html
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Sequences to GenBank<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Helpful Mesquite features<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/index.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" --><!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/informationStrips.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Matrix information strips<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/installation.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Installation<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Interpreting Results<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/knownIssues.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Known Issues<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/limitations.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Limitations<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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2 changes: 1 addition & 1 deletion Source/mesquite/chromaseq/aChromaseqIntro/manual/listWindow.html
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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->List window features<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Matrix Colors<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Chromatogram Navigation <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Chromaseq and other programs <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Overview<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Phred &amp; Phrap Options<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Post-Phrap Options <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Preparation &amp; Processing<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Displaying Primer Sites<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Primer &amp; Gene Information<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Purging Chromaseq Data<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Quality Scores and Colors<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Quickstart<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Running Phred and Phrap <!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
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</table>

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<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Segregating Chromatograms<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Source Code<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Technical FAQ<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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<td width="33%" align="right"><div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Troubleshooting<!-- InstanceEndEditable --></div></td>
<td width="2%">&nbsp;</td>
<td width="14%">Version 1.11<br />
21 August 2014<br /></td>
29 August 2014<br /></td>
</tr>
</table>

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