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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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<title>Clustering tools / software — spectra-cluster toolsuite</title>
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<h1 class="logo logo-name">spectra-cluster toolsuite</h1>
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<p class="blurb">An MS/MS clustering framework</p>
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<ul class="current">
<li class="toctree-l1"><a class="reference internal" href="index.html">Welcome</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Clustering tools / software</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#developing-own-algorithms">Developing own algorithms</a></li>
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<li class="toctree-l1"><a class="reference internal" href="tutorials/proteome_discoverer.html">Proteome Discoverer Tutorial</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/clustering_basics.html">How to cluster MS/MS data</a></li>
<li class="toctree-l1"><a class="reference internal" href="tutorials/unidentified_analysis.html">Analysing proteomics samples using spectrum clustering</a></li>
<li class="toctree-l1"><a class="reference internal" href="analysis_results.html">Analysing clustering results</a></li>
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<div class="section" id="clustering-tools-software">
<h1>Clustering tools / software<a class="headerlink" href="#clustering-tools-software" title="Permalink to this headline">¶</a></h1>
<p>The spectra-cluster toolsuite currently contains four tools to cluster
MS/MS based proteomics data:</p>
<blockquote>
<div><ul class="simple">
<li><a href="#id2"><span class="problematic" id="id3">`Proteome Discoverer node`_</span></a>: Proteome Discoverer node of the spectra-cluster algorithm</li>
<li><a class="reference external" href="https://github.com/spectra-cluster/spectra-cluster-cli">spectra-cluster-cli</a>: Command line version</li>
<li><a class="reference external" href="https://github.com/spectra-cluster/spectra-cluster-gui">spectra-cluster-gui</a>: Graphical user interface</li>
<li><a class="reference external" href="https://github.com/spectra-cluster/spectra-cluster-hadoop">spectra-cluster-hadoop</a>: Hadoop version</li>
</ul>
</div></blockquote>
<p>All of these tools use the <a class="reference external" href="https://github.com/spectra-cluster/spectra-cluster">spectra-cluster Java API</a> to perform the actual
clustering and should produce comparable results.</p>
<p>Our own development focuses on the <a class="reference external" href="https://github.com/spectra-cluster/spectra-cluster-cli">spectra-cluster-cli</a> tool. Therefore, this tool is always at
the latest development stage.</p>
<div class="section" id="developing-own-algorithms">
<h2>Developing own algorithms<a class="headerlink" href="#developing-own-algorithms" title="Permalink to this headline">¶</a></h2>
<p>The spectra-cluster toolsuite provides several ready-to-use APIs that support the
development of MS/MS clustering algorithms as well as own analaysis tools.</p>
<blockquote>
<div><ul class="simple">
<li><a class="reference external" href="https://github.com/spectra-cluster/clustering-file-reader">clustering-file-reader</a>: Java API to read the .clustering format</li>
<li><a class="reference external" href="https://github.com/spectra-cluster/spectra-cluster-py">spectra-cluster-py</a>: Tools to analyse .clustering files as well as
a Python API to process .clustering files</li>
</ul>
</div></blockquote>
<p>The <a class="reference external" href="https://github.com/spectra-cluster/spectra-cluster">spectra-cluster Java API</a> contains the core clustering functionality used by the
implementations of the spectra-cluster algorithm. To test the effect of a, for example,
different spectrum similarity method it is only necessary to implement a single interface.
This new code will then be fully compatible with all existing tools (for example the
<a class="reference external" href="https://github.com/spectra-cluster/spectra-cluster-cli">spectra-cluster-cli</a> command-line interface) which allows the user to immediately test the
new implementation.</p>
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