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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<!-- Copyright (c) 2014 Stijn van Dongen -->
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<title>The&nbsp;MCL&nbsp;family</title>
</head>
<body>
<p style="text-align:right">
16 May 2014&nbsp;&nbsp;&nbsp;
<a class="local" href="mclfamily.ps"><b>mcl</b></a>
14-137
</p>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">1.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#name">NAME</a>
</div>
<div class=" item_compact"><div class=" item_rightalign nowrap " style="right:-3em">2.</div></div>
<div class=" item_text " style="margin-left:4em">
<a class="intern" href="#description">DESCRIPTION</a>
</div>
</div>

<a name="name"></a>
<h2>NAME</h2>
<p style="margin-bottom:0" class="asd_par">
mclfamily &mdash; a description of the mcl family of cluster applications.</p>
<p style="margin-bottom:0" class="asd_par">
<b>mcl</b> is an implementation of the Markov Cluster Algorithm, aka MCL algoritm.
It is described in the <a class="local sibling" href="mcl.html">mcl manual</a>.
Several other applications are part of the MCL distribution. This manual pages
gives an overview.</p>

<a name="description"></a>
<h2>DESCRIPTION</h2>
<div class=" itemize " style="margin-top:1em; font-size:100%">
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcl.html">mcl</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">the cluster algorithm</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mclfaq.html">mclfaq</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">MCL Frequently Asked Questions</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxio.html">mcxio</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">the network/matrix input/output format</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcx.html">mcx</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">general network/matrix tasks</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxdiameter.html">mcx&nbsp;diameter</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">compute diameter of an undirected network</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxctty.html">mcx&nbsp;ctty</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">compute betweenness centrality</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxclcf.html">mcx&nbsp;clcf</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">compute clustering coefficient</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxerdos.html">mcx&nbsp;erdos</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">compute shortest paths in graphs</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxquery.html">mcx&nbsp;query</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">analyse networks at different thresholds</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxalter.html">mcx&nbsp;alter</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">apply network transformations</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxconvert.html">mcx&nbsp;convert</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">convert between interchange/binary storage types</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxarray.html">mcxarray</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">transform array data to MCL matrices</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxdump.html">mcxdump</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">dump a matrix optionally with label substitions</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxload.html">mcxload</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">load label data into matrix and tab files</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxrand.html">mcxrand</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">randomly remove, add, and perturb edge weights</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxmap.html">mcxmap</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">relabel indices in a graph/matrix</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxsubs.html">mcxsubs</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">extracting submatrices in various ways</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxi.html">mcxi</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">general matrix operations</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxassemble.html">mcxassemble</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">create matrices from raw data</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clm.html">clm</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">general graph-clustering related tasks</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmdist.html">clm&nbsp;dist</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">compute split/join distance between clusterings</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmvol.html">clm&nbsp;vol</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">derive node volatility scores from a set of clusterings</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clminfo.html">clm&nbsp;info</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">compute performance measure for clusterings</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmmeet.html">clm&nbsp;meet</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">compute intersection of clusterings</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmmate.html">clm&nbsp;mate</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">find best matching clusters between clusterings</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmclose.html">clm&nbsp;close</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">fetch connected components from graphs or subgraphs</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmimac.html">clm&nbsp;imac</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">interpret MCL iterand/matrix as clustering</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmorder.html">clm&nbsp;order</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">reorder indices to represent blocks from different clusterings</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmresidue.html">clm&nbsp;residue</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">extend subgraph clustering</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="clmformat.html">clmformat</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">display clusters as html or txt files</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mclpipeline.html">mclpipeline</a></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">parsing/assembly/clustering/display</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mclblastline.html">mclblastline</a> <tt>*</tt></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">BLAST pipeline</p>
</div>
<div class=" item_compact"><div class=" item_leftalign nowrap " ><a class="local sibling" href="mcxdeblast.html">mcxdeblast</a> <tt>*</tt></div></div>
<div class=" item_text " style="margin-left:15em">
<p style="margin-top:0em; margin-bottom:0em">parse BLAST files</p>
</div>
</div>
<p style="margin-bottom:0" class="asd_par">
Entries marked <tt>*</tt> are not available if only a default
install is done.</p>
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