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‎docs/index.html‎

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<!DOCTYPE html>
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<html>
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<head>
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<title>EzAAI - Home</title>
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<meta charset="utf-8">
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<meta name="viewport"
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content="width=device-width, initial-scale=1, shrink-to-fit=no">
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<meta http-equiv="X-UA-Compatible" content="IE=edge">
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<link rel="shortcut icon" href="/ezaai/image/ezaai_logowork-16px.ico" type="image/x-icon">
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<link rel="stylesheet" href="/ubcg2/css/style.css">
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href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css"
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integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T"
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crossorigin="anonymous">
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crossorigin="anonymous">
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crossorigin="anonymous"></script>
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crossorigin="anonymous"></script>
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<script
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src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js"
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integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM"
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crossorigin="anonymous"></script>
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<script>
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window.dataLayer = window.dataLayer || [];
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function gtag(){dataLayer.push(arguments);}
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gtag('js', new Date());
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gtag('config', 'G-9B3HSS9PWF');
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</script>
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<meta charset="EUC-KR">
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<style>
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.inline-code {
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font-size:85%;
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font-family:SFMono-Regular,Menlo,Monaco,Consolas,Liberation Mono,Courier New,monospace;
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}
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</style>
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</head>
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<body style="padding-left:0;padding-right:0">
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<section>
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<div class="jumbotron">
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<div class="container">
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<img src="/ezaai/image/ezaai_banner.svg" style="max-width:50%;margin-left:auto;margin-right:auto;height:auto;width:auto;display:block">
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<!--
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<h1 class="text-center" style="font-size:4rem">EzAAI</h1>
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</div>
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<h6 class="text-center" style="font-family:serif"><em>A Pipeline for High Throughput Calculation of Prokaryotic Average Amino Acid Identity</em></h6>-->
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</div>
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</div>
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<div class="container p1" style="margin-bottom:5rem">
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<h3 class="text-center" style="font-family:serif"><em>Introduction</em></h3>
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<hr>
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<div class="row">
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<div class="col-10">
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<p>EzAAI is a suite of workflows for improved AAI calculation performance along with the novel module that provides hierarchical clustering analysis.</p>
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<a class="btn btn-outline-primary" href="/ezaai/tutorial" role="button" style="display:inline; margin-right:1rem">
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<i class="fa fa-play-circle-o"></i> Tutorial</a>
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<a class="btn btn-outline-primary" href="/ezaai/download" role="button" style="display:inline; margin-right:1rem">
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<i class="fa fa-download"></i> Download</a>
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<a class="btn btn-outline-primary" href="https://github.com/lebsnu/ezaai" target="_blank" rel="noopener noreferrer" role="button" style="display:inline; margin-right:1rem">
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<i class="fa fa-github"></i> GitHub</a>
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<a class="btn btn-outline-primary" href="/ezaai/citation" role="button" style="display:inline; margin-right:1rem">
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<i class="fa fa-quote-right"></i> Cite us</a>
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</div>
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</div>
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</div>
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<div class="container p1" style="margin-bottom:5rem">
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<h3 class="text-center" style="font-family:serif"><em>Available modules</em></h3>
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<hr>
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<div class="row">
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<div class="col-6">
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<h3>Extract</h3>
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<p><i class="fa fa-check-square-o" style="margin-right:5px"></i> Extracts profile DB from genome using <span class="inline-code">Prodigal</span></p>
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<p>
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<i class="fa fa-code" style="margin-right:5px"></i>
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<span class="inline-code">
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ezaai extract -i &#60;IN&#62; -o &#60;OUT&#62;
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</span>
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</p>
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<table class="table table-sm">
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<thead class="thead-light">
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<tr>
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<th style="width:30%;">Argument</th>
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<th style="width:70%">Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td class="inline-code">-i</td>
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<td>Input bacterial genome sequence</td>
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</tr>
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<tr>
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<td class="inline-code">-o</td>
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<td>Output profile database</td>
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</tr>
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</tbody>
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</table>
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</div>
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<div class="col-6">
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<h3>Convert</h3>
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<p><i class="fa fa-check-square-o" style="margin-right:5px"></i> Converts CDS FASTA file into profile DB</p>
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<p>
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<i class="fa fa-code" style="margin-right:5px"></i>
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<span class="inline-code">ezaai convert -i &#60;IN&#62; -s &#60;SEQ&#62; -o &#60;OUT&#62;</span>
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</p>
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<table class="table table-sm">
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<thead class="thead-light">
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<tr>
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<th style="width:30%;">Argument</th>
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<th style="width:70%">Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td class="inline-code">-i</td>
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<td>Input CDS profile (FASTA format)</td>
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</tr>
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<tr>
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<td class="inline-code">-s</td>
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<td>Sequence type of input file (nucl/prot)</td>
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</tr>
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<tr>
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<td class="inline-code">-o</td>
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<td>Output profile DB</td>
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</tr>
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</tbody>
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</table>
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</div>
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</div>
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<div class="row" style="margin-top:1rem">
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<div class="col-6">
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<h3>Calculate</h3>
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<p><i class="fa fa-check-square-o" style="margin-right:5px"></i> Calculate AAI value from profile databases using MMseqs2</p>
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<p>
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<i class="fa fa-code" style="margin-right:5px"></i>
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<span class="inline-code">
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ezaai calculate -i &#60;IN_1&#62; -j &#60;IN_2&#62; -o &#60;OUT&#62;
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</span>
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</p>
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<table class="table table-sm">
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<thead class="thead-light">
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<tr>
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<th style="width:30%;">Argument</th>
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<th style="width:70%">Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td class="inline-code">-i</td>
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<td>First input profile DB / directory with profile DBs</td>
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</tr>
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<tr>
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<td class="inline-code">-j</td>
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<td>Second input profile DB / directory with profile DBs</td>
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</tr>
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<tr>
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<td class="inline-code">-o</td>
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<td>Output result file</td>
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</tr>
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</tbody>
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</table>
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</div>
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<div class="col-6">
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<h3>Cluster</h3>
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<p><i class="fa fa-check-square-o" style="margin-right:5px"></i> Hierarchical clustering of taxa with AAI values</p>
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<p>
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<i class="fa fa-code" style="margin-right:5px"></i>
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<span class="inline-code">
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ezaai cluster -i &#60;IN&#62; -o &#60;OUT&#62;
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</span>
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</p>
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<table class="table table-sm">
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<thead class="thead-light">
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<tr>
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<th style="width:30%;">Argument</th>
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<th style="width:70%">Description</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td class="inline-code">-i</td>
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<td>Input EzAAI result file containing all-by-all pairwise AAI values</td>
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</tr>
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<tr>
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<td class="inline-code">-o</td>
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<td>Output result file</td>
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</tr>
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</tbody>
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</table>
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</div>
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</div>
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</div>
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<div class="container p1" style="margin-bottom:5rem">
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<h2 style="margin-top:2rem;margin-bottom:1rem;text-align:center;font-family:serif"><em>EzAAI TEAM</em></h2>
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<div class="row" style="text-align: center">
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<div class="col-md-8">
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<div class="border-bottom" style="padding-left:1rem;padding-right:1rem">
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<h3>Contributors</h3>
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</div>
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</div>
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<div class="col-md-4">
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<div class="border-bottom" style="padding-left:1rem;padding-right:1rem">
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<h3>CA <a href="mailto:jchun@snu.ac.kr" target="_top" style="color:black"><i class="fa fa-envelope-o" style="font-size:70%"></i></a></h3>
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</div>
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</div>
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</div>
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<div class="row" style="text-align: center;">
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<div class="col-md-4">
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<div style="margin:1rem 1rem">
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<div class="profile_image">
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<img src="/homepage/images/team/DWkim.jpg" style="width:150px">
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</div>
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<h5>Dongwook Kim<sup style="font-size:60%">1</sup></h5>
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</div>
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</div>
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<div class="col-md-4">
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<div style="margin:1rem 1rem">
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<div class="profile_image">
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<img src="/homepage/images/team/sein.jpg" style="width:150px">
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</div>
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<h5>Sein Park<sup style="font-size:60%">1</sup></h5>
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</div>
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</div>
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<div class="col-md-4">
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<div style="margin:1rem 1rem">
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<div class="profile_image">
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<img src="/ezaai/image/jon.jpg" style="width:150px">
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</div>
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<h5>Jon Jongsik Chun<sup style="font-size:60%">1,2,3</sup></h5>
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</div>
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</div>
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</div>
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<div style="margin-bottom:3rem">
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<p style="margin-top:0!important;margin-bottom:0;font-size:80%"><sup>1 </sup>Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, Republic of Korea</p>
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<p style="margin-top:0!important;margin-bottom:0;font-size:80%"><sup>2 </sup>Institute of Molecular Biology and Genetics, Seoul National University, Seoul 00826, Republic of Korea</p>
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<p style="margin-top:0!important;margin-bottom:0;font-size:80%"><sup>3 </sup>School of Biological Sciences, Seoul National University, Seoul 00826, Republic of Korea</p>
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</div>
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</div>
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</section>
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<nav class="navbar navbar-expand-md navbar-dark fixed-top bg-dark">
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<div class="container">
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<div class="navbar-header">
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<a class="navbar-brand" href="/ezaai"><img src="/ezaai/image/ezaai_logowork-160px.svg" width="30"> EzAAI</a>
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<li class="nav-item"><a class="nav-link" href="/ezaai">Home</a></li>
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<li class="nav-item"><a class="nav-link" href="/ezaai/tutorial">Tutorial</a></li>
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<li class="nav-item"><a class="nav-link" href="/ezaai/download">Download</a></li>
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<li class="nav-item"><a class="nav-link" href="https://github.com/lebsnu/ezaai" target="_blank" rel="noopener noreferrer"><i class="fa fa-github"></i> GitHub</a></li>
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<li class="nav-item"><a class="nav-link" href="/ezaai/data">Data</a></li>
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<li class="nav-item"><a class="nav-link" href="/ezaai/citation">Cite us</a></li>
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$(document).ready(function() {
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<footer class="footer align-middle" style="padding:0 0;z-index:5">
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<p style="height:3rem; margin-top:1rem!important">&copy; <a class="a-footer" href="http://leb.snu.ac.kr/" target="_blank" rel="noopener noreferrer">Laboratory of Evolutionary Bioinformatics</a>, Seoul
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National University. 2021-</p>
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