changingAlignmentFormats.html

<h1 id="changing-alignment-formats">Changing alignment formats</h1>
<p>There are many different formats for storing alignments in files.</p>
<p>Formats that can be read by many (but not all) phylogenetic software include:</p>
<ul class="incremental">
<li><a href="http://en.wikipedia.org/wiki/FASTA_format">fasta</a></li>
<li><a href="http://en.wikipedia.org/wiki/Nexus_file">nexus</a> (which can be used to store much more than just alignment data)</li>
<li><a href="http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format">phylip</a> (both interleaved and sequential)</li>
</ul>
<p>To convert from fasta to phylip format you could use:</p>
<ul class="incremental">
<li><a href="http://phylogeny.lirmm.fr/phylo_cgi/data_converter.cgi">Phylogeny.fr data converter</a> (works going from fasta to phylip interleaved for use by PhyML)</li>
<li><a href="http://www.clustal.org/download/clustalx_help.html">ClustalX</a></li>
</ul>