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<h1 class="title-article" id="articleContentId">基因家族扩张与收缩分析-CAFE5</h1>
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<p><img alt="" height="540" src="https://img-blog.csdnimg.cn/7046d4f291bb406e8ee4cb92c11bd5af.png" width="818"></p>
<p><strong>CAFE</strong>(Computational Analysis of gene Family Evolution)是一款<strong>以解释系统发育历史的方式分析基因家族大小变化</strong>的软件，这种分析常被称为基因家族收缩扩张(Gene family expansions and contractions)分析。</p>
<p><span style="color:#79c6cd;">CAFE使用出生和死亡过程来模拟用户指定的系统发育树中的基因获得和丢失</span>，可计算由父节点到子节点的基因家族大小转移率，也可推断祖先物种的基因家族大小，在该模型下生成的基因家族规模分布可以为评估观察到的类群之间家族规模差异的显著性提供基础。</p>
<p>自2005年Hahn课题组提出评估基因家族进化速度和模式的算法，2006年第一个版本CAFE发表后，2020年推出了最新版本<a href="https://academic.oup.com/bioinformatics/article-abstract/36/22-23/5516/6039105?redirectedFrom=fulltext" rel="nofollow" title="CAFE5">CAFE5</a>，之前旧版本的基本模型假设所有基因家族都具有相同的进化速率。新版本支持伽马分布速率类别对家族之间的速率变化进行显式建模。2020年发表，相较于cafe4来讲操作更加方便并且新增了<strong>模型(Gamma)</strong>。</p>
<p><a class="link-info" href="https://github.com/hahnlab/CAFE5/releases" title="CAFE5下载">CAFE5下载</a></p>
<h2><a name="t0"></a>1.安装</h2>
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<pre data-index="0" class="set-code-show" name="code"><code class="hljs language-cobol"><ol class="hljs-ln" style="width:100%"><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="1"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">git clone https:<span class="hljs-operator">/</span><span class="hljs-operator">/</span>github.com<span class="hljs-operator">/</span>hahnlab<span class="hljs-operator">/</span>CAFE<span class="hljs-number">5</span>.git</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="2"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">cd CAFE<span class="hljs-number">5</span></div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="3"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">.<span class="hljs-operator">/</span>configure</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="4"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">make</div></div></li></ol></code><div class="hljs-button {2}" data-title="复制" onclick="hljs.copyCode(event)"></div></pre>
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<h2><a name="t1"></a>2.cafe5的使用</h2>
<p>输入文件至少要两个，一个是基因家族数目统计文件<strong>Genefamilies_Count.tsv</strong>，一个是树文件<strong>tree.txt</strong>（带有分化时间），还可以增加一个lambda文件</p>
<h3><a name="t2"></a>2.1 常用参数</h3>
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<pre data-index="1" class="set-code-show" name="code"><code class="hljs language-cobol"><ol class="hljs-ln" style="width:1129px"><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="1"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">--infile, -i</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="2"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line"> </div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="3"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">Path <span class="hljs-keyword">to</span> tab <span class="hljs-keyword">delimited</span> gene families <span class="hljs-keyword">file</span> <span class="hljs-keyword">to</span> be analyzed<span class="hljs-operator"> - </span>Required <span class="hljs-keyword">for</span> estimation.</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="4"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line"> </div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="5"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">--n_gamma_cats, -k</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="6"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line"> </div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="7"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line"><span class="hljs-keyword">Number</span> <span class="hljs-keyword">of</span> gamma categories <span class="hljs-keyword">to</span> <span class="hljs-keyword">use</span>. <span class="hljs-keyword">If</span> specified, the Gamma model will be used <span class="hljs-keyword">to</span> <span class="hljs-keyword">run</span> calculations; otherwise the Base model will be used.</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="8"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line"> </div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="9"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">--pvalue, -P</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="10"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line"> </div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="11"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">P-value <span class="hljs-keyword">to</span> <span class="hljs-keyword">use</span> <span class="hljs-keyword">for</span> determining significance <span class="hljs-keyword">of</span> family <span class="hljs-keyword">size</span> change, <span class="hljs-keyword">Default</span><span class="hljs-operator">=</span><span class="hljs-number">0.05</span>.</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="12"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line"> </div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="13"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">--tree, -t</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="14"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line"> </div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="15"></div></div><div class="hljs-ln-code"><div class="hljs-ln-line">Path <span class="hljs-keyword">to</span> <span class="hljs-keyword">file</span> containing newick formatted tree<span class="hljs-operator"> - </span>Required <span class="hljs-keyword">for</span> estimation.</div></div></li><li><div class="hljs-ln-numbers"><div class="hljs-ln-line hljs-ln-n" data-line-number="16"></div></
