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justincbagley authored Apr 3, 2019
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<p>Scripts for file processing and analysis in phylogenomics &amp; phylogeography</p>


<!-- <h4><p><strong><font color="orange">** WARNING! PIrANHA v0.2-alpha.1c is a pre-release version of a new release that involves a complete rewrite of PIrANHA. PLEASE DO NOT DOWNLOAD THIS RELEASE!!! **</font></strong></p>
<!-- <h4><p><strong><font color="orange">** WARNING! PIrANHA v0.2-alpha.2 is a pre-release version of a new release that involves a complete rewrite of PIrANHA. PLEASE DO NOT DOWNLOAD THIS RELEASE!!! **</font></strong></p>
</h4> -->
<p><strong><font color="orange">** WARNING! PIrANHA v0.2-alpha.1c is a pre-release version of a new release that involves a complete rewrite of PIrANHA that is still under development. PLEASE DO NOT DOWNLOAD THIS RELEASE!!! **</font></strong></p>
<p><strong><font color="orange">** WARNING! PIrANHA v0.2-alpha.2 is a pre-release version of a new release that involves a complete rewrite of PIrANHA that is still under development. PLEASE DO NOT DOWNLOAD THIS RELEASE!!! **</font></strong></p>
<p><font color="orange">This pre-release (and all upcoming alpha versions) is only available publicly to ease issues related to <i>lack</i> of support for Homebrew taps for private repositories (e.g. deprecated solutions).</font></p>

<h2 id="license">LICENSE</h2>
<p>All code within the <code class="highlighter-rouge">PIrANHA</code> v0.2-alpha.1c repository is available “AS IS” under a 3-Clause BSD license. See the <a href="/PIrANHA/LICENSE">LICENSE</a> file for more information.</p>
<p>All code within the <code class="highlighter-rouge">PIrANHA</code> v0.2-alpha.2 repository is available “AS IS” under a 3-Clause BSD license. See the <a href="/PIrANHA/LICENSE">LICENSE</a> file for more information.</p>

<h2 id="citation">CITATION</h2>
<p>If you use scripts from this repository as part of your published research, I require that you cite the repository as follows (also see DOI information below):</p>
<ul>
<li>Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub repository, Available at: <a href="https://github.com/justincbagley/piranha">http://github.com/justincbagley/PIrANHA</a>.</li>
<li>Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub repository, Available at: <a href="https://github.com/justincbagley/piranha">http://github.com/justincbagley/PIrANHA</a>.</li>
</ul>

<p>Alternatively, please provide the following link to this software repository in your manuscript:</p>
Expand All @@ -187,7 +187,7 @@ <h2 id="citation">CITATION</h2>

<h2 id="doi">DOI</h2>
<p>The DOI for <code class="highlighter-rouge">PIrANHA</code>, via <a href="https://zenodo.org">Zenodo</a>, is as follows: <a href="https://doi.org/10.5281/zenodo.890815"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.890815.svg" alt="DOI" /></a>. Here are some examples of citing PIrANHA using the DOI:</p>
<p>Bagley, J.C. 2019. PIrANHA v0.2-alpha.1c. GitHub package, Available at: <a href="http://doi.org/10.5281/zenodo.596766">http://doi.org/10.5281/zenodo.596766</a>.</p>
<p>Bagley, J.C. 2019. PIrANHA v0.2-alpha.2. GitHub package, Available at: <a href="http://doi.org/10.5281/zenodo.596766">http://doi.org/10.5281/zenodo.596766</a>.</p>
<p>Bagley, J.C. 2019. PIrANHA. Zenodo, Available at: <a href="http://doi.org/10.5281/zenodo.596766">http://doi.org/10.5281/zenodo.596766</a>.</p>

<h2 id="documentation">DOCUMENTATION</h2>
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