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<!DOCTYPE html>
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<head>
<meta charset="UTF-8">
<title>Sequence Matrix by gaurav</title>
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<section class="page-header">
<h1 class="project-name">Sequence Matrix</h1>
<h2 class="project-tagline">Assemble multigene/multitaxon phylogenetic datasets easily</h2>
<a href="https://github.com/gaurav/taxondna" class="btn">View on GitHub</a>
<a href="https://github.com/gaurav/taxondna/releases/latest" class="btn">Download latest release</a>
<a href="https://github.com/gaurav/taxondna/zipball/master" class="btn">Download source as .zip</a>
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</section>
<section class="main-content">
<p>Sequence Matrix allows you to easily concatenate gene datasets. A spreadsheet-like interface displays what you've assembled so far; TNT, Nexus, FASTA and Mega files can be dragged into the application to add them. Your entire dataset can be exported as TNT or Nexus files.</p>
<p>To find out more, please see our <a href="http://www.youtube.com/watch?v=Adwr-CZdNOM">introductory screencast</a> of Sequence Matrix on YouTube. We've also <a href="http://www.slideshare.net/mrvaidya/sequence-matrix-gene-concatenation-made-easy-4797559">made available a presentation on Sequence Matrix</a> (delivered to the Hennig XXVIII conference in June 2009) and <a href="http://dx.doi.org/10.1111/j.1096-0031.2010.00329.x">the paper we wrote</a> describing Sequence Matrix in Cladistics. </p>
<center>
<iframe width="560" height="315" src="https://www.youtube.com/embed/Adwr-CZdNOM" frameborder="0" allowfullscreen></iframe>
</center>
<h1>
<a id="for-users-of-macos-x" class="anchor" href="#for-users-of-macos-x" aria-hidden="true"><span class="octicon octicon-link"></span></a>For users of MacOS X
</h1>
<p>If you get an "unidentified developer" error, please right-click on the file and select "Open": you should get the some error, but with an "Open" button that allows you to bypass it. Alternatively, you can change your security settings: go to System Preferences on your Mac, click on "Security & Privacy" and go to the "General" tab. If you set "All apps downloaded from:" to "Anywhere", Sequence Matrix should run without any problem.</p>
<h1>
<a id="testimonials" class="anchor" href="#testimonials" aria-hidden="true"><span class="octicon octicon-link"></span></a>Testimonials</h1>
<p>Here are some reviews of Sequence Matrix we've spotted around the internet.</p>
<ul>
<li><p>"Thanks so much. This software has saved me many hours of tedious work." -- <a href="http://www.youtube.com/user/evanmelstad">evanmelstad</a> on <a href="http://www.youtube.com/comment?lc=bOaM8sE6UvMNa2ZilLgH45-Uti1e3fwDMQ2dXEtzNXQ">YouTube</a>.</p></li>
<li>
<p>"It is a real pain combining matrices from different loci, particularly when you have taxa represented in one matrix and not in another. I’ve usually done this by hand and it gets tedious. I recently stumbled across a Java tool that makes this process quite simple: SequenceMatrix." -- <a href="http://lacertilia.com/?p=1420">The Glor Lab</a>, University of Rochester. </p>
</li>
<li>
<p>"... the 12 individual gene alignments were concatenated using the software SequenceMatrix v1.7.6 (Vaidya et al., 2011) to create a master alignment of 10,836 bp total, equivalent to roughly 65% of the mtDNA genome." -- <em><a href="http://dx.doi.org/10.1016/j.ympev.2011.03.025">Pleistocene diversification of living squirrel monkeys (Saimiri spp.) inferred from complete mitochondrial genome sequences</a></em> by Kenneth L. Chioua, Luca Pozzia, Jessica W. Lynch Alfaroc and Anthony Di Fiore. </p>
</li>
</ul>
<h1>What about Species Identifier?</h1>
<p>Species Identifier is no longer being actively maintained. If you want to
repeat the analyses in
<a href="http://dx.doi.org/10.1080/10635150600969864">Meier <em>et al</em>, 2006</a>,
you can download <a href="https://github.com/gaurav/taxondna/releases/latest">the latest release</a>.
</p>
<h1>
<a id="problems-let-us-know" class="anchor" href="#problems-let-us-know" aria-hidden="true"><span class="octicon octicon-link"></span></a>Problems? Let us know!</h1>
<p>If you find any bugs in this or any other release, please <a href="https://github.com/gaurav/taxondna/issues">report them to us</a>! The source code for this project is available <a href="http://github.com/gaurav/taxondna">on GitHub</a>.</p>
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<span class="site-footer-owner"><a href="https://github.com/gaurav/taxondna">Sequence Matrix</a> is maintained by <a href="https://github.com/gaurav">gaurav</a>.</span>
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