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<!Doctype html>
<html>
<head>
<meta charset="UTF-8" />
<title>Seqphase</title>
<link rel="stylesheet" href="style.css"/>
</head>
<body>
<a href="https://github.com/eeg-ebe/SeqPHASE">
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</svg>
</a>
<div class="contentdiv">
<h1>SeqPHASE</h1>
<p id="cite">Flot (2010) <strong>SeqPHASE: a web tool for interconverting PHASE input/output files and FASTA sequence alignments </strong> <em>Molecular Ecology Ressources</em> <strong>10</strong> (1): 162-166 [<a href="http://dx.doi.org/10.1111/j.1755-0998.2009.02732.x">link</a>]</p><br>
<div class="navigation">
<a href="index.html">Back to startpage</a>
<a href="faq.html">FAQ</a>
<a href="examples.zip">Download examples</a>
<a href="step1.html">Step 1</a>
<a href="mailto: jflot@ulb.ac.be">E-Mail the author</a>
</div>
<h2>Step 2: converting PHASE output files into FASTA alignments</h2>
<table>
<tr class="option">
<td>PHASE output file (.out or .out_pairs)</td>
<td> </td>
<td><input id="phaseOutFile" type="file" autocomplete="off"></td>
</tr>
<tr class="description">
<td colspan="3">
<p>If a .out file is inputted, a list of phased haplotypes will be returned as FASTA with 1-letter indetermination code letters (R, W, M, Y, S or K) at positions where phase certainty is inferior to a certain threshold (90% if PHASE default running options were used).</p>
<p>If a .out_pairs file is inputted, a list of all possible haplotype pairs for each individual will be returned as FASTA with their respective probabilities shown between parentheses.</p>
</td>
</tr>
<tr class="option">
<td>Constant positions file (.const), if any</td>
<td> </td>
<td>
<span id="passedSpan" style="display: none">
<span id="passedConstFileContent"></span>
<a id="changePassedConstFile">Change</a>
</span>
<input id="constFile" autocomplete="off" type="file">
<input type="hidden" id="completePassedConstFileContent" autocomplete="off" value=""/>
</td>
</tr>
<tr class="description">
<td colspan="3">
<p>If no .const file is inputted, the FASTA alignment will only contain variable positions.</p>
<p id="passedDescription" style="display: none">The content of the .const file was passed from step 1. Only the first 12 to 15 characters are visible.</p>
</td>
</tr>
<tr class="option">
<td>Sort sequences</td>
<td> </td>
<td><input id="sortSequences" type="checkbox" autocomplete="off" checked="checked"></td>
</tr>
<tr class="description">
<td colspan="3">
<p>Sort sequences in alphabetical order.</p>
</td>
</tr>
<tr class="option">
<td>Reduce sequences</td>
<td> </td>
<td><input id="reduceSequences" type="checkbox" autocomplete="off" checked="checked"></td>
</tr>
<tr class="description">
<td colspan="3">
<p>Reduce output (recommended for some downstream applications, such as phylogenetic analyses)</p>
</td>
</tr>
</table>
<span class="middle">
<button id="runJob2Button">Run SeqPHASE</button>
<button id="resetJob2Button">Reset Form</button>
<span>
<div id="resultArea" style="display: none">
<p>A FASTA alignment of phased haplotypes has been generated. In this file, each of the two
haplotypes inferred from a sequence are given the name of that sequence followed by a or b.
The posterior probability of each haplotype is shown in parentheses after its name. In case
there are several alternative haplotype reconstructions, then all possible haplotypes are
listed.</p>
<a id="downloadLink" download="phased.fasta">Click here to download the generated Fasta file</a>
</div>
<br>
<br>
<div class="navigation">
<a href="index.html">Back to startpage</a>
<a href="faq.html">FAQ</a>
<a href="examples.zip">Download examples</a>
<a href="step1.html">Step 1</a>
<a href="mailto: jflot@ulb.ac.be">E-Mail the author</a>
</div>
</div>
<script src="seqphase2.js" type="text/javascript"></script>
<script src="step2.js" type="text/javascript"></script>
</body>
</html>