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Fabio Mendes
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Updated .html files, added all webpage sections
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‎docs/citation.html‎

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<ul>
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<li class="nav"><a class="nav" href="index.html">HOME</a></li>
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<li class="nav"><a class="nav" href="download.html">DOWNLOAD</a></li>
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<li class="nav"><a class="nav" href="">MANUAL</a></li>
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<li class="nav"><a class="nav" href="">FAQ</a></li>
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<li class="nav"><a class="nav" href="manual.html">MANUAL</a></li>
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<li class="nav"><a class="nav" href="faq.html">FAQ</a></li>
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<li class="nav"><a class="nav" href="">CITATION</a></li>
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<li class="nav"><a class="nav" href="">CONTACT</a></li>
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<li class="nav"><a class="nav" href="contact.html">CONTACT</a></li>
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</ul>
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</nav>
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</div>
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<div class="content grid_8">
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<h1>Citation</h1>
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<p>The most recent citation for CAFE is:</p>
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<p>The citation for CAFE v3.1 and v4.0 is:</p>
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<p class="indented">Han, M. V., Thomas, G. W. C., Lugo-Martinez, J., and Hahn, M. W. Estimating gene gain and loss rates in the presence of error in genome assembly and annotation using CAFE 3. <i>Molecular Biology and Evolution 30</i>, 8 (2013)</p>
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<p>The citation for CAFE v2.0 is:</p>
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<p class="indented">Hahn, M. W., Demuth, J. P., and Han, S. -G. Accelerated rate of gene gain and loss in primates. <i>Genetics 177</i>, (2007)</p>
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<p>Original development of the statistical framework and algorithms implemented in CAFE are published in:</p>
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<p class="indented">Hahn, M. W., DeBie, T., Stajich, J. E., Nguyen, C., and Cristianini, N. Estimating the tempo and mode of gene family from comparative genomic data. <i>Genomic Research 15</i>, 8 (2005)</p>
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<p class="indented">DeBie, T., Cristianini, N., Demuth, J. P., and Hahn, M. W. CAFE: a computational tool for the study of gene family evolution. <i>Bioinformatics 22</i> (2006)
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</div>
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‎docs/contact.html‎

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<!DOCTYPE html>
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<html>
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<head>
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<title>CAFE</title>
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<link rel="stylesheet" type="text/css" href="css/960_12_col.css"/>
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<link rel="stylesheet" type="text/css" href="css/elements.css"/>
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</head>
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<body>
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<div class="container_12">
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<div class="logo grid_12">
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<img src="images/cafe_logo2.png" alt="CAFE software"
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width="391.6"/>
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</div>
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<div class="menulogo grid_4">
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<nav>
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<ul>
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<li class="nav"><a class="nav" href="index.html">HOME</a></li>
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<li class="nav"><a class="nav" href="download.html">DOWNLOAD</a></li>
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<li class="nav"><a class="nav" href="manual.html">MANUAL</a></li>
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<li class="nav"><a class="nav" href="faq.html">FAQ</a></li>
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<li class="nav"><a class="nav" href="citation.html">CITATION</a></li>
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<li class="nav"><a class="nav" href="">CONTACT</a></li>
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</ul>
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</nav>
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</div>
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<div class="content grid_8">
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<h1>Contact</h1>
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<p>If you are in need of assistance or want to ask us a question, please research the threads in (or post a new thread to) CAFE's Google <a href="https://groups.google.com/forum/#!forum/hahnlabcafe" target="_blank">Group.</a></p>
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</div>
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<div class="foot grid_12">
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<img src="images/cafe_footer.png" width="940"/>
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</html>

‎docs/download.html‎

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<nav>
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<ul>
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<li class="nav"><a class="nav" href="index.html">HOME</a></li>
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<li class="nav"><a class="nav" href="download.html">DOWNLOAD</a></li>
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<li class="nav"><a class="nav" href="">MANUAL</a></li>
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<li class="nav"><a class="nav" href="">FAQ</a></li>
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<li class="nav"><a class="nav" href="">DOWNLOAD</a></li>
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<li class="nav"><a class="nav" href="manual.html">MANUAL</a></li>
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<li class="nav"><a class="nav" href="faq.html">FAQ</a></li>
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<li class="nav"><a class="nav" href="citation.html">CITATION</a></li>
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<li class="nav"><a class="nav" href="">CONTACT</a></li>
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<li class="nav"><a class="nav" href="contact.html">CONTACT</a></li>
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<h1>Downloading and installing CAFE</h1>
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<h2>Download</h2>
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<p>CAFE's files can be downloaded in two different ways:</p>
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<ol>
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<li class="downl">Download the latest release tarball <a href="https://github.com/hahnlab/CAFE/archive/v3.1.tar.gz">here</a>, put the tarball in a folder of your choice, and from that folder extract the files with command (replacing "some_version" with the version you downloaded):</li>
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<p style="text-indent: 1em;"><font size="-1" face="Courier New">$ tar -zxvf CAFE-some_version.tar.gz</font></p>
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<li class="downl">If you have <font face="Courier New">git</font> installed, you can clone CAFE's repository by moving to a directory of your choice and entering the command:</li>
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<p style="text-indent: 1em;"><font size=-1" face="Courier New">$ git clone https://github.com/hahnlab/CAFE.git</p>
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<p style="text-indent: 1em;"><font size=-1" face="Courier New">$ git clone https://github.com/hahnlab/CAFE.git</font></p>
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</ol>
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<h2>Installation</h2>
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<p>CAFE comes with a precompiled executable file (<font size"-1" face="Courier New">/path/to/CAFE/release/cafe</font>) that should work on Linux machines.
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If you prefer to compile from source yourself, move to the CAFE folder, and run:</p>
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<p style="text-indent: 1em;"><font size="-1" face="Courier New">$ make</font></p>
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<p>Then just copy the binary file to somewhere on your path, such as <font face="Courier New">/usr/local/bin/</font>.
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Alternatively, add <font face="Courier New">/path/to/CAFE/release/</font> to your <font face="Courier New">$PATH</font> variable (in your <font face="Courier New">.bashrc</font> or <font face="Courier New">.bash_profile)</font>.
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</p>
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‎docs/faq.html‎

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<title>CAFE</title>
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<body>
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<div class="container_12">
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<div class="logo grid_12">
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<img src="images/cafe_logo2.png" alt="CAFE software"
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width="391.6"/>
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</div>
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<div class="menulogo grid_4">
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<nav>
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<ul>
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<li class="nav"><a class="nav" href="index.html">HOME</a></li>
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<li class="nav"><a class="nav" href="download.html">DOWNLOAD</a></li>
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<li class="nav"><a class="nav" href="manual.html">MANUAL</a></li>
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<li class="nav"><a class="nav" href="">FAQ</a></li>
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<li class="nav"><a class="nav" href="citation.html">CITATION</a></li>
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<li class="nav"><a class="nav" href="contact.html">CONTACT</a></li>
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</ul>
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</nav>
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<div class="content grid_8">
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<h1>FAQ</h1>
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<p>Under construction!</p>
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</div>
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<img src="images/cafe_footer.png" width="940"/>
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‎docs/index.html‎

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<ul>
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<li class="nav"><a class="nav" href="">HOME</a></li>
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<li class="nav"><a class="nav" href="download.html">DOWNLOAD</a></li>
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<li class="nav"><a class="nav" href="">MANUAL</a></li>
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<li class="nav"><a class="nav" href="">FAQ</a></li>
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<li class="nav"><a class="nav" href="manual.html">MANUAL</a></li>
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<li class="nav"><a class="nav" href="faq.html">FAQ</a></li>
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<li class="nav"><a class="nav" href="citation.html">CITATION</a></li>
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<li class="nav"><a class="nav" href="">CONTACT</a></li>
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<li class="nav"><a class="nav" href="contact.html">CONTACT</a></li>
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<h1>Announcements</h1>
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<h2>Sep 27, 2016</h2>
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<p>Pellentesque habitant morbi tristique senectus et netus et malesuada fames ac turpis egestas. Vestibulum tortor quam, feugiat vitae, ultricies eget, tempor sit amet, ante. Donec eu libero sit amet quam egestas semper. Aenean ultricies mi vitae est. Mauris placerat eleifend leo. Quisque sit amet est et sapien ullamcorper pharetra. Vestibulum erat wisi, condimentum sed, commodo vitae, ornare sit amet, wisi. Aenean fermentum, elit eget tincidunt condimentum, eros ipsum rutrum orci, sagittis tempus lacus enim ac dui. Donec non enim in turpis pulvinar facilisis. Ut felis. Praesent dapibus, neque id cursus faucibus, tortor neque egestas augue, eu vulputate magna eros eu erat. Aliquam erat volutpat. Nam dui mi, tincidunt quis, accumsan porttitor, facilisis luctus, metus</p>
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<h2>Mar 17, 2017</h2>
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<p>CAFE v4.0 coming out soon!</p>
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‎docs/manual.html‎

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<!DOCTYPE html>
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<html>
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<title>CAFE</title>
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<link rel="stylesheet" type="text/css" href="css/960_12_col.css"/>
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<link rel="stylesheet" type="text/css" href="css/elements.css"/>
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</head>
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<body>
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<div class="container_12">
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<div class="logo grid_12">
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<img src="images/cafe_logo2.png" alt="CAFE software"
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width="391.6"/>
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</div>
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<div class="menulogo grid_4">
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<nav>
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<ul>
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<li class="nav"><a class="nav" href="index.html">HOME</a></li>
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<li class="nav"><a class="nav" href="download.html">DOWNLOAD</a></li>
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<li class="nav"><a class="nav" href="">MANUAL</a></li>
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<li class="nav"><a class="nav" href="faq.html">FAQ</a></li>
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<li class="nav"><a class="nav" href="citation.html">CITATION</a></li>
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<li class="nav"><a class="nav" href="contact.html">CONTACT</a></li>
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<h1>Manual</h1>
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<p>Please find the links to the manual and tutorial .pdf files below, as well as the files required for the tutorial (if you want to download them, right-click on the link &rarr; "Save link as"):</p>
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<ul>
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<li class="downl_un">Manual <a href="https://github.com/hahnlab/CAFE/blob/master/docs/cafe_manual.pdf" target="_blank">.pdf</a></li>
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<li class="downl_un">Tutorial <a href="">.pdf</a></li>
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<li class="downl_un">Tutorial files <a href="">.tar.gz</a></li>
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</ul>
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</div>
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<img src="images/cafe_footer.png" width="940"/>
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</body>
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</html>

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