<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Perform Divergence Stratigraphy — divergence_stratigraphy • orthologr</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Perform Divergence Stratigraphy — divergence_stratigraphy"><meta property="og:description" content="This function takes a query organism and performs
divergence stratigraphy (Quint et al.,2012 ; Drost et al. 2015) against a
closely related subject organism."><meta property="og:image" content="/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body data-spy="scroll" data-target="#toc">
    

    <div class="container template-reference-topic">
      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">orthologr</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.4.2</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"><li>
  <a href="../reference/index.html">Reference</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    Articles
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu"><li>
      <a href="../articles/Install.html">Installing Prerequisite Tools</a>
    </li>
    <li>
      <a href="../articles/blast.html">BLAST searches using orthologr</a>
    </li>
    <li>
      <a href="../articles/dNdS_estimation.html">Orthology inference dNdS estimation of orthologous genes using orthologr</a>
    </li>
    <li>
      <a href="../articles/divergence_stratigraphy.html">Performing Divergence Stratigraphy</a>
    </li>
    <li>
      <a href="../articles/orthology_inference.html">Orthology Inference using orthologr</a>
    </li>
    <li>
      <a href="../articles/sequence_alignments.html">Sequence alignments with orthologr</a>
    </li>
  </ul></li>
<li>
  <a href="../news/index.html">Changelog</a>
</li>
      </ul><ul class="nav navbar-nav navbar-right"><li>
  <a href="https://github.com/drostlab/orthologr/" class="external-link">
    <span class="fab fa-github fa-lg"></span>
     
  </a>
</li>
      </ul></div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      

      </header><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Perform Divergence Stratigraphy</h1>
    <small class="dont-index">Source: <a href="https://github.com/drostlab/orthologr/blob/HEAD/R/divergence_stratigraphy.R" class="external-link"><code>R/divergence_stratigraphy.R</code></a></small>
    <div class="hidden name"><code>divergence_stratigraphy.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>This function takes a query organism and performs
divergence stratigraphy (Quint et al.,2012 ; Drost et al. 2015) against a
closely related subject organism.</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">divergence_stratigraphy</span><span class="op">(</span></span>
<span>  <span class="va">query_file</span>,</span>
<span>  <span class="va">subject_file</span>,</span>
<span>  aligner <span class="op">=</span> <span class="st">"diamond"</span>,</span>
<span>  eval <span class="op">=</span> <span class="st">"1E-5"</span>,</span>
<span>  ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>,</span>
<span>  dnds_est.method <span class="op">=</span> <span class="st">"Comeron"</span>,</span>
<span>  delete_corrupt_cds <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  aligner_path <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  comp_cores <span class="op">=</span> <span class="fl">1</span>,</span>
<span>  dnds.threshold <span class="op">=</span> <span class="fl">2</span>,</span>
<span>  store_locally <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  quiet <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  clean_folders <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  ds.values <span class="op">=</span> <span class="cn">TRUE</span>,</span>
<span>  subject.id <span class="op">=</span> <span class="cn">FALSE</span>,</span>
<span>  n_quantile <span class="op">=</span> <span class="fl">10</span>,</span>
<span>  sensitivity_mode <span class="op">=</span> <span class="st">"fast"</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>query_file</dt>
<dd><p>a character string specifying the path to the CDS file of interest (query organism).</p></dd>


<dt>subject_file</dt>
<dd><p>a character string specifying the path to the CDS file of interest (subject organism).</p></dd>


<dt>aligner</dt>
<dd><p>a character string specifying the sequence aligner. The options are <code>diamond</code> and <code>blast</code>.
The option <code>diamond</code> uses DIAMOND2 which is up to 10 000X folds faster than BLASTP while retaining the sensitivity of BLASTP.
Thus, the default is <code>aligner</code> = <code>diamond</code>.</p></dd>


<dt>eval</dt>
<dd><p>a numeric value specifying the E-Value cutoff for DIAMOND or BLAST hit detection.</p></dd>


<dt>ortho_detection</dt>
<dd><p>a character string specifying the orthology inference method that shall be performed
to detect orthologous genes. Default is <code>ortho_detection</code> = "RBH" (DIAMOND or BLAST reciprocal best hit).
Available methods are: "BH" (DIAMOND or BLAST best hit), "RBH" (DIAMOND or BLAST reciprocal best hit).</p></dd>


<dt>dnds_est.method</dt>
<dd><p>the dNdS estimation method that shall be used.
Options are:</p><ul><li><p><code>dnds_est.method = "Comeron"</code> (Default): Comeron's method (1995)</p></li>
<li><p><code>dnds_est.method = "Li"</code>: Li's method (1993)</p></li>
<li><p><code>dnds_est.method = "NG"</code>: Nei, M. and Gojobori, T. (1986)</p></li>
<li><p><code>dnds_est.method = "LWL"</code>: Li, W.H., et al. (1985)</p></li>
<li><p><code>dnds_est.method = "LPB"</code>: Li, W.H. (1993) and Pamilo, P. and Bianchi, N.O. (1993)</p></li>
<li><p><code>dnds_est.method = "MLWL"</code>: (Modified LWL), MLPB (Modified LPB): Tzeng, Y.H., et al. (2004)</p></li>
<li><p><code>dnds_est.method = "YN"</code>: Yang, Z. and Nielsen, R. (2000)</p></li>
<li><p><code>dnds_est.method ="MYN"</code> (Modified YN): Zhang, Z., et al. (2006)</p></li>
</ul></dd>


<dt>delete_corrupt_cds</dt>
<dd><p>a logical value indicating whether sequences with corrupt base triplets should be removed from the input <code>file</code>. This is the case when the length of coding sequences cannot be divided by 3 and thus the coding sequence contains at least one corrupt base triplet.</p></dd>


<dt>aligner_path</dt>
<dd><p>a character string specifying the path to the DIAMOND or BLAST program (in case you don't use the default path).</p></dd>


<dt>comp_cores</dt>
<dd><p>a numeric value specifying the number of cores that shall be used to perform
parallel computations on a multicore machine.</p></dd>


<dt>dnds.threshold</dt>
<dd><p>a numeric value specifying the dnds threshold for genes that shall be retained.
Hence all genes having a dNdS value &lt;= <code>dnds.threshold</code> are retained. Default is <code>dnds.threshold</code> = 2.</p></dd>


<dt>store_locally</dt>
<dd><p>a logical value indicating whether or not alignment files shall be stored locally rather than in <code><a href="https://rdrr.io/r/base/tempfile.html" class="external-link">tempdir()</a></code>.</p></dd>


<dt>quiet</dt>
<dd><p>a logical value specifying whether a successful interface call shall be printed out to the console.</p></dd>


<dt>clean_folders</dt>
<dd><p>a logical value specifying whether the internal folder structure shall be deleted (cleaned) after
processing this function. Default is <code>clean_folders</code> = <code>FALSE</code>.</p></dd>


<dt>ds.values</dt>
<dd><p>a logical value specifying whether divergence stratum values (ds values) or dNdS values shall be returned
by <code>divergence_stratigraphy</code>. Default is <code>ds.values</code> = <code>TRUE</code>.</p></dd>


<dt>subject.id</dt>
<dd><p>a logical value indicating whether <code>query_id</code> AND <code>subject_id</code> should be returned.</p></dd>


<dt>n_quantile</dt>
<dd><p>a numeric value specifying the number of quantiles that should be returned.</p></dd>


<dt>sensitivity_mode</dt>
<dd><p>specify the level of alignment sensitivity, when using DIAMOND2. The higher the sensitivity level, the more deep homologs can be found, but at the cost of reduced computational speed.
- sensitivity_mode = "faster" : fastest alignment mode, but least sensitive (default). Designed for finding hits of &gt;70
- sensitivity_mode = "default" : Default mode. Designed for finding hits of &gt;70
- sensitivity_mode = "fast" : fast alignment mode, but least sensitive (default). Designed for finding hits of &gt;70
- sensitivity_mode = "mid-sensitive" : fast alignments between the fast mode and the sensitive mode in sensitivity.
- sensitivity_mode = "sensitive" : fast alignments, but full sensitivity for hits &gt;40
- sensitivity_mode = "more-sensitive" : more sensitive than the sensitive mode.
- sensitivity_mode = "very-sensitive" : sensitive alignment mode.
- sensitivity_mode = "ultra-sensitive" : most sensitive alignment mode (sensitivity as high as BLASTP).</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>A data.table storing the divergence map of the query organism.</p>
    </div>
    <div id="details">
    <h2>Details</h2>
    <p>Introduced by Quint et al., 2012 and extended in Drost et al. 2015, divergence stratigraphy
 is the process of quantifying the selection pressure (in terms of amino acid sequence divergence) acting on
 orthologous genes between closely related species. The resulting sequence divergence map (short divergence map),
 stores the divergence stratum in the first column and the query_id of inferred orthologous genes in the second column.</p> 
<p>Following steps are performed to obtain a standard divergence map based on divergence_stratigraphy:</p> 
<p>Divergence Stratigraphy:</p> 
<p></p><ul><li><p>1) Orthology Inference using DIAMOND or BLAST reciprocal best hit ("RBH") based on blastp</p></li>
<li><p>2) Pairwise global amino acid alignments of orthologous genes using the Needleman-Wunsch algorithm</p></li>
<li><p>3) Codon alignments of orthologous genes using PAL2NAL</p></li>
<li><p>4) dNdS estimation using Comeron's method (1995)</p></li>
<li><p>5) Assigning dNdS values to divergence strata (deciles)</p></li>
</ul></div>
    <div id="note">
    <h2>Note</h2>
    <p>Although this function has been heavily optimized and parallelized, performing
Divergence Stratigraphy using two genomes will take some computation time.</p>
<p>In our experience performing Divergence Stratigraphy using two genomes (one query and one subject genome)
on an 8 core machine can take up to 1,5 - 2 hours.</p>
    </div>
    <div id="references">
    <h2>References</h2>
    <p>Quint M et al. (2012). A transcriptomic hourglass in plant embryogenesis. Nature (490): 98-101.</p> 
<p>Drost HG et al. (2015). Evidence for Active Maintenance of Phylotranscriptomic Hourglass Patterns in Animal and Plant Embryogenesis. Mol Biol Evol. 32 (5): 1221-1231 doi:10.1093/molbev/msv012</p>
    </div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p><code><a href="dNdS.html">dNdS</a></code>, <code><a href="divergence_map.html">divergence_map</a></code>,<code><a href="substitutionrate.html">substitutionrate</a></code>, <code><a href="multi_aln.html">multi_aln</a></code>,
  <code><a href="codon_aln.html">codon_aln</a></code>, <code><a href="diamond_best.html">diamond_best</a></code>, <code><a href="diamond_rec.html">diamond_rec</a></code>,
  <code><a href="codon_aln.html">codon_aln</a></code>, <code><a href="blast_best.html">blast_best</a></code>, <code><a href="blast_rec.html">blast_rec</a></code>, 
  <code><a href="map_generator_dnds.html">map_generator_dnds</a></code></p></div>
    </div>
    <div id="author">
    <h2>Author</h2>
    <p>Hajk-Georg Drost and Jaruwatana Sodai Lotharukpong</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="co"># performing standard divergence stratigraphy</span></span></span>
<span class="r-in"><span> <span class="fu">divergence_stratigraphy</span><span class="op">(</span></span></span>
<span class="r-in"><span>      query_file      <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_thal_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      subject_file    <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_lyra_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      eval            <span class="op">=</span> <span class="st">"1E-5"</span>,</span></span>
<span class="r-in"><span>      ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>, </span></span>
<span class="r-in"><span>      comp_cores      <span class="op">=</span> <span class="fl">1</span>, </span></span>
<span class="r-in"><span>      quiet           <span class="op">=</span> <span class="cn">TRUE</span>, </span></span>
<span class="r-in"><span>      clean_folders   <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span> <span class="co"># performing standard divergence stratigraphy using the aligner_path argument to specify</span></span></span>
<span class="r-in"><span> <span class="co"># the path to diamond</span></span></span>
<span class="r-in"><span> <span class="fu">divergence_stratigraphy</span><span class="op">(</span></span></span>
<span class="r-in"><span>      query_file      <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_thal_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      subject_file    <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_lyra_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      eval            <span class="op">=</span> <span class="st">"1E-5"</span>, </span></span>
<span class="r-in"><span>      ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>,</span></span>
<span class="r-in"><span>      aligner_path    <span class="op">=</span> <span class="st">"path/to/diamond"</span>,</span></span>
<span class="r-in"><span>      comp_cores      <span class="op">=</span> <span class="fl">1</span>, </span></span>
<span class="r-in"><span>      quiet           <span class="op">=</span> <span class="cn">TRUE</span>, </span></span>
<span class="r-in"><span>      clean_folders   <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> <span class="co"># Divergence Stratigraphy can also be performed in parallel </span></span></span>
<span class="r-in"><span> <span class="co"># (on a multicore machine) using the 'comp_cores' argument</span></span></span>
<span class="r-in"><span> <span class="fu">divergence_stratigraphy</span><span class="op">(</span></span></span>
<span class="r-in"><span>      query_file      <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_thal_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      subject_file    <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_lyra_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      eval            <span class="op">=</span> <span class="st">"1E-5"</span>, </span></span>
<span class="r-in"><span>      ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>, </span></span>
<span class="r-in"><span>      comp_cores      <span class="op">=</span> <span class="fl">2</span>, </span></span>
<span class="r-in"><span>      quiet           <span class="op">=</span> <span class="cn">TRUE</span>, </span></span>
<span class="r-in"><span>      clean_folders   <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> <span class="co"># in case you want a divergence map with DS values and query_id and subject_id</span></span></span>
<span class="r-in"><span> <span class="co"># you can specify subject.id = TRUE</span></span></span>
<span class="r-in"><span> <span class="co"># performing standard divergence stratigraphy</span></span></span>
<span class="r-in"><span> <span class="fu">divergence_stratigraphy</span><span class="op">(</span></span></span>
<span class="r-in"><span>      query_file      <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_thal_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      subject_file    <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_lyra_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      eval            <span class="op">=</span> <span class="st">"1E-5"</span>,</span></span>
<span class="r-in"><span>      ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>, </span></span>
<span class="r-in"><span>      comp_cores      <span class="op">=</span> <span class="fl">1</span>, </span></span>
<span class="r-in"><span>      quiet           <span class="op">=</span> <span class="cn">TRUE</span>, </span></span>
<span class="r-in"><span>      clean_folders   <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
<span class="r-in"><span>      subject.id      <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span> <span class="co"># in case you want a divergence map with KaKs values and query_id and subject_id</span></span></span>
<span class="r-in"><span> <span class="co"># you can specify ds.values = FALSE and subject.id = TRUE</span></span></span>
<span class="r-in"><span> <span class="co"># performing standard divergence stratigraphy</span></span></span>
<span class="r-in"><span> <span class="fu">divergence_stratigraphy</span><span class="op">(</span></span></span>
<span class="r-in"><span>      query_file      <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_thal_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      subject_file    <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_lyra_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      eval            <span class="op">=</span> <span class="st">"1E-5"</span>,</span></span>
<span class="r-in"><span>      ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>, </span></span>
<span class="r-in"><span>      comp_cores      <span class="op">=</span> <span class="fl">1</span>, </span></span>
<span class="r-in"><span>      quiet           <span class="op">=</span> <span class="cn">TRUE</span>, </span></span>
<span class="r-in"><span>      clean_folders   <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
<span class="r-in"><span>      subject.id      <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span> <span class="co"># in case you want a divergence map with divergence stratum as quintile (5-quantile) values </span></span></span>
<span class="r-in"><span> <span class="co"># or any other N-quantile values rather than the default decile (10-quantile) values,</span></span></span>
<span class="r-in"><span> <span class="co"># you can specify this with n_quantile.</span></span></span>
<span class="r-in"><span> <span class="fu">divergence_stratigraphy</span><span class="op">(</span></span></span>
<span class="r-in"><span>      query_file      <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_thal_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      subject_file    <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">'seqs/ortho_lyra_cds.fasta'</span>, package <span class="op">=</span> <span class="st">'orthologr'</span><span class="op">)</span>,</span></span>
<span class="r-in"><span>      eval            <span class="op">=</span> <span class="st">"1E-5"</span>,</span></span>
<span class="r-in"><span>      ortho_detection <span class="op">=</span> <span class="st">"RBH"</span>, </span></span>
<span class="r-in"><span>      comp_cores      <span class="op">=</span> <span class="fl">1</span>, </span></span>
<span class="r-in"><span>      quiet           <span class="op">=</span> <span class="cn">TRUE</span>, </span></span>
<span class="r-in"><span>      clean_folders   <span class="op">=</span> <span class="cn">TRUE</span>,</span></span>
<span class="r-in"><span>      n_quantile      <span class="op">=</span> <span class="fl">5</span><span class="op">)</span></span></span>
<span class="r-in"><span>      </span></span>
<span class="r-in"><span> <span class="op">}</span></span></span>
<span class="r-in"><span> </span></span>
</code></pre></div>
    </div>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
    </nav></div>
</div>


      <footer><div class="copyright">
  <p></p><p>Developed by Hajk-Georg Drost.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>

      </footer></div>

  


  

  </body></html>

