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<h1 class="epydoc">Source Code for <a href="Bio.Phylo.PAML._parse_baseml-module.html">Module Bio.Phylo.PAML._parse_baseml</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno">  1</tt>  <tt class="py-line"><tt class="py-comment"># Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)</tt> </tt>
<a name="L2"></a><tt class="py-lineno">  2</tt>  <tt class="py-line"><tt class="py-comment"># This code is part of the Biopython distribution and governed by its</tt> </tt>
<a name="L3"></a><tt class="py-lineno">  3</tt>  <tt class="py-line"><tt class="py-comment"># license. Please see the LICENSE file that should have been included</tt> </tt>
<a name="L4"></a><tt class="py-lineno">  4</tt>  <tt class="py-line"><tt class="py-comment"># as part of this package.</tt> </tt>
<a name="L5"></a><tt class="py-lineno">  5</tt>  <tt class="py-line"> </tt>
<a name="L6"></a><tt class="py-lineno">  6</tt>  <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> </tt>
<a name="L7"></a><tt class="py-lineno">  7</tt>  <tt class="py-line"> </tt>
<a name="L8"></a><tt class="py-lineno">  8</tt>  <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable Bio.Phylo.PAML._parse_baseml.line_floats_re=Bio.Phylo.PAML._parse_baseml-module.html#line_floats_re,Variable Bio.Phylo.PAML._parse_codeml.line_floats_re=Bio.Phylo.PAML._parse_codeml-module.html#line_floats_re"><a title="Bio.Phylo.PAML._parse_baseml.line_floats_re
Bio.Phylo.PAML._parse_codeml.line_floats_re" class="py-name" href="#" onclick="return doclink('link-0', 'line_floats_re', 'link-0');">line_floats_re</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">"-*\d+\.\d+"</tt><tt class="py-op">)</tt> </tt>
<a name="L9"></a><tt class="py-lineno">  9</tt>  <tt class="py-line"> </tt>
<a name="parse_basics"></a><div id="parse_basics-def"><a name="L10"></a><tt class="py-lineno"> 10</tt> <a class="py-toggle" href="#" id="parse_basics-toggle" onclick="return toggle('parse_basics');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.PAML._parse_baseml-module.html#parse_basics">parse_basics</a><tt class="py-op">(</tt><tt class="py-param">lines</tt><tt class="py-op">,</tt> <tt class="py-param">results</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_basics-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_basics-expanded"><a name="L11"></a><tt class="py-lineno"> 11</tt>  <tt class="py-line">    <tt class="py-docstring">"""Parse the basics that should be present in most baseml results files.</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt>  <tt class="py-line">    <tt class="py-name">version_re</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">"BASEML \(in paml version (\d+\.\d+[a-z]*).*"</tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt>  <tt class="py-line">    <tt class="py-name">np_re</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">"lnL\(ntime:\s+\d+\s+np:\s+(\d+)\)"</tt><tt class="py-op">)</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt>  <tt class="py-line">    <tt class="py-name">num_params</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt>  <tt class="py-line">        <tt class="py-comment"># Find all floating point numbers in this line</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt>  <tt class="py-line">        <tt class="py-name">line_floats_res</tt> <tt class="py-op">=</tt> <tt id="link-1" class="py-name"><a title="Bio.Phylo.PAML._parse_baseml.line_floats_re
Bio.Phylo.PAML._parse_codeml.line_floats_re" class="py-name" href="#" onclick="return doclink('link-1', 'line_floats_re', 'link-0');">line_floats_re</a></tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt>  <tt class="py-line">        <tt class="py-name">line_floats</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line_floats_res</tt><tt class="py-op">]</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt>  <tt class="py-line">        <tt class="py-comment"># Find the version number</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt>  <tt class="py-line">        <tt class="py-comment"># Example match: </tt> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt>  <tt class="py-line">        <tt class="py-comment"># "BASEML (in paml version 4.3, August 2009)  alignment.phylip"</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt>  <tt class="py-line">        <tt class="py-name">version_res</tt> <tt class="py-op">=</tt> <tt class="py-name">version_re</tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-2', 'match', 'link-2');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">version_res</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt>  <tt class="py-line">            <tt id="link-3" class="py-name" targets="Variable Bio.Restriction.Restriction.AanI.results=Bio.Restriction.Restriction.AanI-class.html#results,Variable Bio.Restriction.Restriction.AarI.results=Bio.Restriction.Restriction.AarI-class.html#results,Variable Bio.Restriction.Restriction.AasI.results=Bio.Restriction.Restriction.AasI-class.html#results,Variable Bio.Restriction.Restriction.AatI.results=Bio.Restriction.Restriction.AatI-class.html#results,Variable Bio.Restriction.Restriction.AatII.results=Bio.Restriction.Restriction.AatII-class.html#results,Variable Bio.Restriction.Restriction.AbsI.results=Bio.Restriction.Restriction.AbsI-class.html#results,Variable Bio.Restriction.Restriction.Acc16I.results=Bio.Restriction.Restriction.Acc16I-class.html#results,Variable Bio.Restriction.Restriction.Acc36I.results=Bio.Restriction.Restriction.Acc36I-class.html#results,Variable Bio.Restriction.Restriction.Acc65I.results=Bio.Restriction.Restriction.Acc65I-class.html#results,Variable Bio.Restriction.Restriction.AccB1I.results=Bio.Restriction.Restriction.AccB1I-class.html#results,Variable Bio.Restriction.Restriction.AccB7I.results=Bio.Restriction.Restriction.AccB7I-class.html#results,Variable Bio.Restriction.Restriction.AccBSI.results=Bio.Restriction.Restriction.AccBSI-class.html#results,Variable Bio.Restriction.Restriction.AccI.results=Bio.Restriction.Restriction.AccI-class.html#results,Variable Bio.Restriction.Restriction.AccII.results=Bio.Restriction.Restriction.AccII-class.html#results,Variable Bio.Restriction.Restriction.AccIII.results=Bio.Restriction.Restriction.AccIII-class.html#results,Variable Bio.Restriction.Restriction.AceIII.results=Bio.Restriction.Restriction.AceIII-class.html#results,Variable Bio.Restriction.Restriction.AciI.results=Bio.Restriction.Restriction.AciI-class.html#results,Variable Bio.Restriction.Restriction.AclI.results=Bio.Restriction.Restriction.AclI-class.html#results,Variable Bio.Restriction.Restriction.AclWI.results=Bio.Restriction.Restriction.AclWI-class.html#results,Variable Bio.Restriction.Restriction.AcoI.results=Bio.Restriction.Restriction.AcoI-class.html#results,Variable Bio.Restriction.Restriction.AcsI.results=Bio.Restriction.Restriction.AcsI-class.html#results,Variable Bio.Restriction.Restriction.AcuI.results=Bio.Restriction.Restriction.AcuI-class.html#results,Variable Bio.Restriction.Restriction.AcvI.results=Bio.Restriction.Restriction.AcvI-class.html#results,Variable Bio.Restriction.Restriction.AcyI.results=Bio.Restriction.Restriction.AcyI-class.html#results,Variable Bio.Restriction.Restriction.AdeI.results=Bio.Restriction.Restriction.AdeI-class.html#results,Variable Bio.Restriction.Restriction.AfaI.results=Bio.Restriction.Restriction.AfaI-class.html#results,Variable Bio.Restriction.Restriction.AfeI.results=Bio.Restriction.Restriction.AfeI-class.html#results,Variable Bio.Restriction.Restriction.AfiI.results=Bio.Restriction.Restriction.AfiI-class.html#results,Variable Bio.Restriction.Restriction.AflII.results=Bio.Restriction.Restriction.AflII-class.html#results,Variable Bio.Restriction.Restriction.AflIII.results=Bio.Restriction.Restriction.AflIII-class.html#results,Variable Bio.Restriction.Restriction.AgeI.results=Bio.Restriction.Restriction.AgeI-class.html#results,Variable Bio.Restriction.Restriction.AgsI.results=Bio.Restriction.Restriction.AgsI-class.html#results,Variable Bio.Restriction.Restriction.AhaIII.results=Bio.Restriction.Restriction.AhaIII-class.html#results,Variable Bio.Restriction.Restriction.AhdI.results=Bio.Restriction.Restriction.AhdI-class.html#results,Variable Bio.Restriction.Restriction.AhlI.results=Bio.Restriction.Restriction.AhlI-class.html#results,Variable Bio.Restriction.Restriction.AjiI.results=Bio.Restriction.Restriction.AjiI-class.html#results,Variable Bio.Restriction.Restriction.AjnI.results=Bio.Restriction.Restriction.AjnI-class.html#results,Variable Bio.Restriction.Restriction.AjuI.results=Bio.Restriction.Restriction.AjuI-class.html#results,Variable Bio.Restriction.Restriction.AleI.results=Bio.Restriction.Restriction.AleI-class.html#results,Variable Bio.Restriction.Restriction.AlfI.results=Bio.Restriction.Restriction.AlfI-class.html#results,Variable Bio.Restriction.Restriction.AloI.results=Bio.Restriction.Restriction.AloI-class.html#results,Variable Bio.Restriction.Restriction.AluBI.results=Bio.Restriction.Restriction.AluBI-class.html#results,Variable Bio.Restriction.Restriction.AluI.results=Bio.Restriction.Restriction.AluI-class.html#results,Variable Bio.Restriction.Restriction.Alw21I.results=Bio.Restriction.Restriction.Alw21I-class.html#results,Variable Bio.Restriction.Restriction.Alw26I.results=Bio.Restriction.Restriction.Alw26I-class.html#results,Variable Bio.Restriction.Restriction.Alw44I.results=Bio.Restriction.Restriction.Alw44I-class.html#results,Variable Bio.Restriction.Restriction.AlwFI.results=Bio.Restriction.Restriction.AlwFI-class.html#results,Variable Bio.Restriction.Restriction.AlwI.results=Bio.Restriction.Restriction.AlwI-class.html#results,Variable Bio.Restriction.Restriction.AlwNI.results=Bio.Restriction.Restriction.AlwNI-class.html#results,Variable Bio.Restriction.Restriction.Ama87I.results=Bio.Restriction.Restriction.Ama87I-class.html#results,Variable Bio.Restriction.Restriction.Aor13HI.results=Bio.Restriction.Restriction.Aor13HI-class.html#results,Variable Bio.Restriction.Restriction.Aor51HI.results=Bio.Restriction.Restriction.Aor51HI-class.html#results,Variable Bio.Restriction.Restriction.ApaBI.results=Bio.Restriction.Restriction.ApaBI-class.html#results,Variable Bio.Restriction.Restriction.ApaI.results=Bio.Restriction.Restriction.ApaI-class.html#results,Variable Bio.Restriction.Restriction.ApaLI.results=Bio.Restriction.Restriction.ApaLI-class.html#results,Variable Bio.Restriction.Restriction.ApeKI.results=Bio.Restriction.Restriction.ApeKI-class.html#results,Variable Bio.Restriction.Restriction.ApoI.results=Bio.Restriction.Restriction.ApoI-class.html#results,Variable Bio.Restriction.Restriction.ApyPI.results=Bio.Restriction.Restriction.ApyPI-class.html#results,Variable Bio.Restriction.Restriction.AquII.results=Bio.Restriction.Restriction.AquII-class.html#results,Variable Bio.Restriction.Restriction.AquIII.results=Bio.Restriction.Restriction.AquIII-class.html#results,Variable Bio.Restriction.Restriction.AquIV.results=Bio.Restriction.Restriction.AquIV-class.html#results,Variable Bio.Restriction.Restriction.ArsI.results=Bio.Restriction.Restriction.ArsI-class.html#results,Variable Bio.Restriction.Restriction.AscI.results=Bio.Restriction.Restriction.AscI-class.html#results,Variable Bio.Restriction.Restriction.AseI.results=Bio.Restriction.Restriction.AseI-class.html#results,Variable Bio.Restriction.Restriction.Asi256I.results=Bio.Restriction.Restriction.Asi256I-class.html#results,Variable Bio.Restriction.Restriction.AsiGI.results=Bio.Restriction.Restriction.AsiGI-class.html#results,Variable Bio.Restriction.Restriction.AsiSI.results=Bio.Restriction.Restriction.AsiSI-class.html#results,Variable Bio.Restriction.Restriction.Asp700I.results=Bio.Restriction.Restriction.Asp700I-class.html#results,Variable Bio.Restriction.Restriction.Asp718I.results=Bio.Restriction.Restriction.Asp718I-class.html#results,Variable Bio.Restriction.Restriction.AspA2I.results=Bio.Restriction.Restriction.AspA2I-class.html#results,Variable Bio.Restriction.Restriction.AspCNI.results=Bio.Restriction.Restriction.AspCNI-class.html#results,Variable Bio.Restriction.Restriction.AspEI.results=Bio.Restriction.Restriction.AspEI-class.html#results,Variable Bio.Restriction.Restriction.AspI.results=Bio.Restriction.Restriction.AspI-class.html#results,Variable Bio.Restriction.Restriction.AspLEI.results=Bio.Restriction.Restriction.AspLEI-class.html#results,Variable Bio.Restriction.Restriction.AspS9I.results=Bio.Restriction.Restriction.AspS9I-class.html#results,Variable Bio.Restriction.Restriction.AssI.results=Bio.Restriction.Restriction.AssI-class.html#results,Variable Bio.Restriction.Restriction.AsuC2I.results=Bio.Restriction.Restriction.AsuC2I-class.html#results,Variable Bio.Restriction.Restriction.AsuHPI.results=Bio.Restriction.Restriction.AsuHPI-class.html#results,Variable Bio.Restriction.Restriction.AsuI.results=Bio.Restriction.Restriction.AsuI-class.html#results,Variable Bio.Restriction.Restriction.AsuII.results=Bio.Restriction.Restriction.AsuII-class.html#results,Variable Bio.Restriction.Restriction.AsuNHI.results=Bio.Restriction.Restriction.AsuNHI-class.html#results,Variable Bio.Restriction.Restriction.AvaI.results=Bio.Restriction.Restriction.AvaI-class.html#results,Variable Bio.Restriction.Restriction.AvaII.results=Bio.Restriction.Restriction.AvaII-class.html#results,Variable Bio.Restriction.Restriction.AvaIII.results=Bio.Restriction.Restriction.AvaIII-class.html#results,Variable Bio.Restriction.Restriction.AviII.results=Bio.Restriction.Restriction.AviII-class.html#results,Variable Bio.Restriction.Restriction.AvrII.results=Bio.Restriction.Restriction.AvrII-class.html#results,Variable Bio.Restriction.Restriction.AxyI.results=Bio.Restriction.Restriction.AxyI-class.html#results,Variable Bio.Restriction.Restriction.BaeGI.results=Bio.Restriction.Restriction.BaeGI-class.html#results,Variable Bio.Restriction.Restriction.BaeI.results=Bio.Restriction.Restriction.BaeI-class.html#results,Variable Bio.Restriction.Restriction.BalI.results=Bio.Restriction.Restriction.BalI-class.html#results,Variable Bio.Restriction.Restriction.BamHI.results=Bio.Restriction.Restriction.BamHI-class.html#results,Variable Bio.Restriction.Restriction.BanI.results=Bio.Restriction.Restriction.BanI-class.html#results,Variable Bio.Restriction.Restriction.BanII.results=Bio.Restriction.Restriction.BanII-class.html#results,Variable Bio.Restriction.Restriction.BanIII.results=Bio.Restriction.Restriction.BanIII-class.html#results,Variable Bio.Restriction.Restriction.BarI.results=Bio.Restriction.Restriction.BarI-class.html#results,Variable Bio.Restriction.Restriction.BasI.results=Bio.Restriction.Restriction.BasI-class.html#results,Variable Bio.Restriction.Restriction.BauI.results=Bio.Restriction.Restriction.BauI-class.html#results,Variable Bio.Restriction.Restriction.BbeI.results=Bio.Restriction.Restriction.BbeI-class.html#results,Variable Bio.Restriction.Restriction.Bbr7I.results=Bio.Restriction.Restriction.Bbr7I-class.html#results,Variable Bio.Restriction.Restriction.BbrPI.results=Bio.Restriction.Restriction.BbrPI-class.html#results,Variable Bio.Restriction.Restriction.BbsI.results=Bio.Restriction.Restriction.BbsI-class.html#results,Variable Bio.Restriction.Restriction.BbuI.results=Bio.Restriction.Restriction.BbuI-class.html#results,Variable Bio.Restriction.Restriction.Bbv12I.results=Bio.Restriction.Restriction.Bbv12I-class.html#results,Variable Bio.Restriction.Restriction.BbvCI.results=Bio.Restriction.Restriction.BbvCI-class.html#results,Variable Bio.Restriction.Restriction.BbvI.results=Bio.Restriction.Restriction.BbvI-class.html#results,Variable Bio.Restriction.Restriction.BbvII.results=Bio.Restriction.Restriction.BbvII-class.html#results,Variable Bio.Restriction.Restriction.BccI.results=Bio.Restriction.Restriction.BccI-class.html#results,Variable Bio.Restriction.Restriction.Bce83I.results=Bio.Restriction.Restriction.Bce83I-class.html#results,Variable Bio.Restriction.Restriction.BceAI.results=Bio.Restriction.Restriction.BceAI-class.html#results,Variable Bio.Restriction.Restriction.BcefI.results=Bio.Restriction.Restriction.BcefI-class.html#results,Variable Bio.Restriction.Restriction.BcgI.results=Bio.Restriction.Restriction.BcgI-class.html#results,Variable Bio.Restriction.Restriction.BciVI.results=Bio.Restriction.Restriction.BciVI-class.html#results,Variable Bio.Restriction.Restriction.BclI.results=Bio.Restriction.Restriction.BclI-class.html#results,Variable Bio.Restriction.Restriction.BcnI.results=Bio.Restriction.Restriction.BcnI-class.html#results,Variable Bio.Restriction.Restriction.BcuI.results=Bio.Restriction.Restriction.BcuI-class.html#results,Variable Bio.Restriction.Restriction.BdaI.results=Bio.Restriction.Restriction.BdaI-class.html#results,Variable Bio.Restriction.Restriction.BetI.results=Bio.Restriction.Restriction.BetI-class.html#results,Variable Bio.Restriction.Restriction.BfaI.results=Bio.Restriction.Restriction.BfaI-class.html#results,Variable Bio.Restriction.Restriction.BfiI.results=Bio.Restriction.Restriction.BfiI-class.html#results,Variable Bio.Restriction.Restriction.BfmI.results=Bio.Restriction.Restriction.BfmI-class.html#results,Variable Bio.Restriction.Restriction.BfoI.results=Bio.Restriction.Restriction.BfoI-class.html#results,Variable Bio.Restriction.Restriction.BfrI.results=Bio.Restriction.Restriction.BfrI-class.html#results,Variable Bio.Restriction.Restriction.BfuAI.results=Bio.Restriction.Restriction.BfuAI-class.html#results,Variable Bio.Restriction.Restriction.BfuCI.results=Bio.Restriction.Restriction.BfuCI-class.html#results,Variable Bio.Restriction.Restriction.BfuI.results=Bio.Restriction.Restriction.BfuI-class.html#results,Variable Bio.Restriction.Restriction.BglI.results=Bio.Restriction.Restriction.BglI-class.html#results,Variable Bio.Restriction.Restriction.BglII.results=Bio.Restriction.Restriction.BglII-class.html#results,Variable Bio.Restriction.Restriction.BinI.results=Bio.Restriction.Restriction.BinI-class.html#results,Variable Bio.Restriction.Restriction.BisI.results=Bio.Restriction.Restriction.BisI-class.html#results,Variable Bio.Restriction.Restriction.BlnI.results=Bio.Restriction.Restriction.BlnI-class.html#results,Variable Bio.Restriction.Restriction.BlpI.results=Bio.Restriction.Restriction.BlpI-class.html#results,Variable Bio.Restriction.Restriction.BlsI.results=Bio.Restriction.Restriction.BlsI-class.html#results,Variable Bio.Restriction.Restriction.BmcAI.results=Bio.Restriction.Restriction.BmcAI-class.html#results,Variable Bio.Restriction.Restriction.Bme1390I.results=Bio.Restriction.Restriction.Bme1390I-class.html#results,Variable Bio.Restriction.Restriction.Bme18I.results=Bio.Restriction.Restriction.Bme18I-class.html#results,Variable Bio.Restriction.Restriction.BmeRI.results=Bio.Restriction.Restriction.BmeRI-class.html#results,Variable Bio.Restriction.Restriction.BmeT110I.results=Bio.Restriction.Restriction.BmeT110I-class.html#results,Variable Bio.Restriction.Restriction.BmgBI.results=Bio.Restriction.Restriction.BmgBI-class.html#results,Variable Bio.Restriction.Restriction.BmgI.results=Bio.Restriction.Restriction.BmgI-class.html#results,Variable Bio.Restriction.Restriction.BmgT120I.results=Bio.Restriction.Restriction.BmgT120I-class.html#results,Variable Bio.Restriction.Restriction.BmiI.results=Bio.Restriction.Restriction.BmiI-class.html#results,Variable Bio.Restriction.Restriction.BmrFI.results=Bio.Restriction.Restriction.BmrFI-class.html#results,Variable Bio.Restriction.Restriction.BmrI.results=Bio.Restriction.Restriction.BmrI-class.html#results,Variable Bio.Restriction.Restriction.BmsI.results=Bio.Restriction.Restriction.BmsI-class.html#results,Variable Bio.Restriction.Restriction.BmtI.results=Bio.Restriction.Restriction.BmtI-class.html#results,Variable Bio.Restriction.Restriction.BmuI.results=Bio.Restriction.Restriction.BmuI-class.html#results,Variable Bio.Restriction.Restriction.BoxI.results=Bio.Restriction.Restriction.BoxI-class.html#results,Variable Bio.Restriction.Restriction.BpiI.results=Bio.Restriction.Restriction.BpiI-class.html#results,Variable Bio.Restriction.Restriction.BplI.results=Bio.Restriction.Restriction.BplI-class.html#results,Variable Bio.Restriction.Restriction.BpmI.results=Bio.Restriction.Restriction.BpmI-class.html#results,Variable Bio.Restriction.Restriction.Bpu10I.results=Bio.Restriction.Restriction.Bpu10I-class.html#results,Variable Bio.Restriction.Restriction.Bpu1102I.results=Bio.Restriction.Restriction.Bpu1102I-class.html#results,Variable Bio.Restriction.Restriction.Bpu14I.results=Bio.Restriction.Restriction.Bpu14I-class.html#results,Variable Bio.Restriction.Restriction.BpuAI.results=Bio.Restriction.Restriction.BpuAI-class.html#results,Variable Bio.Restriction.Restriction.BpuEI.results=Bio.Restriction.Restriction.BpuEI-class.html#results,Variable Bio.Restriction.Restriction.BpuMI.results=Bio.Restriction.Restriction.BpuMI-class.html#results,Variable Bio.Restriction.Restriction.BpvUI.results=Bio.Restriction.Restriction.BpvUI-class.html#results,Variable Bio.Restriction.Restriction.Bsa29I.results=Bio.Restriction.Restriction.Bsa29I-class.html#results,Variable Bio.Restriction.Restriction.BsaAI.results=Bio.Restriction.Restriction.BsaAI-class.html#results,Variable Bio.Restriction.Restriction.BsaBI.results=Bio.Restriction.Restriction.BsaBI-class.html#results,Variable Bio.Restriction.Restriction.BsaHI.results=Bio.Restriction.Restriction.BsaHI-class.html#results,Variable Bio.Restriction.Restriction.BsaI.results=Bio.Restriction.Restriction.BsaI-class.html#results,Variable Bio.Restriction.Restriction.BsaJI.results=Bio.Restriction.Restriction.BsaJI-class.html#results,Variable Bio.Restriction.Restriction.BsaMI.results=Bio.Restriction.Restriction.BsaMI-class.html#results,Variable Bio.Restriction.Restriction.BsaWI.results=Bio.Restriction.Restriction.BsaWI-class.html#results,Variable Bio.Restriction.Restriction.BsaXI.results=Bio.Restriction.Restriction.BsaXI-class.html#results,Variable Bio.Restriction.Restriction.BsbI.results=Bio.Restriction.Restriction.BsbI-class.html#results,Variable Bio.Restriction.Restriction.Bsc4I.results=Bio.Restriction.Restriction.Bsc4I-class.html#results,Variable Bio.Restriction.Restriction.BscAI.results=Bio.Restriction.Restriction.BscAI-class.html#results,Variable Bio.Restriction.Restriction.BscGI.results=Bio.Restriction.Restriction.BscGI-class.html#results,Variable Bio.Restriction.Restriction.Bse118I.results=Bio.Restriction.Restriction.Bse118I-class.html#results,Variable Bio.Restriction.Restriction.Bse1I.results=Bio.Restriction.Restriction.Bse1I-class.html#results,Variable Bio.Restriction.Restriction.Bse21I.results=Bio.Restriction.Restriction.Bse21I-class.html#results,Variable Bio.Restriction.Restriction.Bse3DI.results=Bio.Restriction.Restriction.Bse3DI-class.html#results,Variable Bio.Restriction.Restriction.Bse8I.results=Bio.Restriction.Restriction.Bse8I-class.html#results,Variable Bio.Restriction.Restriction.BseAI.results=Bio.Restriction.Restriction.BseAI-class.html#results,Variable Bio.Restriction.Restriction.BseBI.results=Bio.Restriction.Restriction.BseBI-class.html#results,Variable Bio.Restriction.Restriction.BseCI.results=Bio.Restriction.Restriction.BseCI-class.html#results,Variable Bio.Restriction.Restriction.BseDI.results=Bio.Restriction.Restriction.BseDI-class.html#results,Variable Bio.Restriction.Restriction.BseGI.results=Bio.Restriction.Restriction.BseGI-class.html#results,Variable Bio.Restriction.Restriction.BseJI.results=Bio.Restriction.Restriction.BseJI-class.html#results,Variable Bio.Restriction.Restriction.BseLI.results=Bio.Restriction.Restriction.BseLI-class.html#results,Variable Bio.Restriction.Restriction.BseMI.results=Bio.Restriction.Restriction.BseMI-class.html#results,Variable Bio.Restriction.Restriction.BseMII.results=Bio.Restriction.Restriction.BseMII-class.html#results,Variable Bio.Restriction.Restriction.BseNI.results=Bio.Restriction.Restriction.BseNI-class.html#results,Variable Bio.Restriction.Restriction.BsePI.results=Bio.Restriction.Restriction.BsePI-class.html#results,Variable Bio.Restriction.Restriction.BseRI.results=Bio.Restriction.Restriction.BseRI-class.html#results,Variable Bio.Restriction.Restriction.BseSI.results=Bio.Restriction.Restriction.BseSI-class.html#results,Variable Bio.Restriction.Restriction.BseX3I.results=Bio.Restriction.Restriction.BseX3I-class.html#results,Variable Bio.Restriction.Restriction.BseXI.results=Bio.Restriction.Restriction.BseXI-class.html#results,Variable Bio.Restriction.Restriction.BseYI.results=Bio.Restriction.Restriction.BseYI-class.html#results,Variable Bio.Restriction.Restriction.BsgI.results=Bio.Restriction.Restriction.BsgI-class.html#results,Variable Bio.Restriction.Restriction.Bsh1236I.results=Bio.Restriction.Restriction.Bsh1236I-class.html#results,Variable Bio.Restriction.Restriction.Bsh1285I.results=Bio.Restriction.Restriction.Bsh1285I-class.html#results,Variable Bio.Restriction.Restriction.BshFI.results=Bio.Restriction.Restriction.BshFI-class.html#results,Variable Bio.Restriction.Restriction.BshNI.results=Bio.Restriction.Restriction.BshNI-class.html#results,Variable Bio.Restriction.Restriction.BshTI.results=Bio.Restriction.Restriction.BshTI-class.html#results,Variable Bio.Restriction.Restriction.BshVI.results=Bio.Restriction.Restriction.BshVI-class.html#results,Variable Bio.Restriction.Restriction.BsiEI.results=Bio.Restriction.Restriction.BsiEI-class.html#results,Variable Bio.Restriction.Restriction.BsiHKAI.results=Bio.Restriction.Restriction.BsiHKAI-class.html#results,Variable Bio.Restriction.Restriction.BsiHKCI.results=Bio.Restriction.Restriction.BsiHKCI-class.html#results,Variable Bio.Restriction.Restriction.BsiI.results=Bio.Restriction.Restriction.BsiI-class.html#results,Variable Bio.Restriction.Restriction.BsiSI.results=Bio.Restriction.Restriction.BsiSI-class.html#results,Variable Bio.Restriction.Restriction.BsiWI.results=Bio.Restriction.Restriction.BsiWI-class.html#results,Variable Bio.Restriction.Restriction.BsiYI.results=Bio.Restriction.Restriction.BsiYI-class.html#results,Variable Bio.Restriction.Restriction.BslFI.results=Bio.Restriction.Restriction.BslFI-class.html#results,Variable Bio.Restriction.Restriction.BslI.results=Bio.Restriction.Restriction.BslI-class.html#results,Variable Bio.Restriction.Restriction.BsmAI.results=Bio.Restriction.Restriction.BsmAI-class.html#results,Variable Bio.Restriction.Restriction.BsmBI.results=Bio.Restriction.Restriction.BsmBI-class.html#results,Variable Bio.Restriction.Restriction.BsmFI.results=Bio.Restriction.Restriction.BsmFI-class.html#results,Variable Bio.Restriction.Restriction.BsmI.results=Bio.Restriction.Restriction.BsmI-class.html#results,Variable Bio.Restriction.Restriction.BsnI.results=Bio.Restriction.Restriction.BsnI-class.html#results,Variable Bio.Restriction.Restriction.Bso31I.results=Bio.Restriction.Restriction.Bso31I-class.html#results,Variable Bio.Restriction.Restriction.BsoBI.results=Bio.Restriction.Restriction.BsoBI-class.html#results,Variable Bio.Restriction.Restriction.Bsp119I.results=Bio.Restriction.Restriction.Bsp119I-class.html#results,Variable Bio.Restriction.Restriction.Bsp120I.results=Bio.Restriction.Restriction.Bsp120I-class.html#results,Variable Bio.Restriction.Restriction.Bsp1286I.results=Bio.Restriction.Restriction.Bsp1286I-class.html#results,Variable Bio.Restriction.Restriction.Bsp13I.results=Bio.Restriction.Restriction.Bsp13I-class.html#results,Variable Bio.Restriction.Restriction.Bsp1407I.results=Bio.Restriction.Restriction.Bsp1407I-class.html#results,Variable Bio.Restriction.Restriction.Bsp143I.results=Bio.Restriction.Restriction.Bsp143I-class.html#results,Variable Bio.Restriction.Restriction.Bsp1720I.results=Bio.Restriction.Restriction.Bsp1720I-class.html#results,Variable Bio.Restriction.Restriction.Bsp19I.results=Bio.Restriction.Restriction.Bsp19I-class.html#results,Variable Bio.Restriction.Restriction.Bsp24I.results=Bio.Restriction.Restriction.Bsp24I-class.html#results,Variable Bio.Restriction.Restriction.Bsp68I.results=Bio.Restriction.Restriction.Bsp68I-class.html#results,Variable Bio.Restriction.Restriction.BspACI.results=Bio.Restriction.Restriction.BspACI-class.html#results,Variable Bio.Restriction.Restriction.BspCNI.results=Bio.Restriction.Restriction.BspCNI-class.html#results,Variable Bio.Restriction.Restriction.BspD6I.results=Bio.Restriction.Restriction.BspD6I-class.html#results,Variable Bio.Restriction.Restriction.BspDI.results=Bio.Restriction.Restriction.BspDI-class.html#results,Variable Bio.Restriction.Restriction.BspEI.results=Bio.Restriction.Restriction.BspEI-class.html#results,Variable Bio.Restriction.Restriction.BspFNI.results=Bio.Restriction.Restriction.BspFNI-class.html#results,Variable Bio.Restriction.Restriction.BspGI.results=Bio.Restriction.Restriction.BspGI-class.html#results,Variable Bio.Restriction.Restriction.BspHI.results=Bio.Restriction.Restriction.BspHI-class.html#results,Variable Bio.Restriction.Restriction.BspLI.results=Bio.Restriction.Restriction.BspLI-class.html#results,Variable Bio.Restriction.Restriction.BspLU11I.results=Bio.Restriction.Restriction.BspLU11I-class.html#results,Variable Bio.Restriction.Restriction.BspMI.results=Bio.Restriction.Restriction.BspMI-class.html#results,Variable Bio.Restriction.Restriction.BspMII.results=Bio.Restriction.Restriction.BspMII-class.html#results,Variable Bio.Restriction.Restriction.BspNCI.results=Bio.Restriction.Restriction.BspNCI-class.html#results,Variable Bio.Restriction.Restriction.BspOI.results=Bio.Restriction.Restriction.BspOI-class.html#results,Variable Bio.Restriction.Restriction.BspPI.results=Bio.Restriction.Restriction.BspPI-class.html#results,Variable Bio.Restriction.Restriction.BspQI.results=Bio.Restriction.Restriction.BspQI-class.html#results,Variable Bio.Restriction.Restriction.BspT104I.results=Bio.Restriction.Restriction.BspT104I-class.html#results,Variable Bio.Restriction.Restriction.BspT107I.results=Bio.Restriction.Restriction.BspT107I-class.html#results,Variable Bio.Restriction.Restriction.BspTI.results=Bio.Restriction.Restriction.BspTI-class.html#results,Variable Bio.Restriction.Restriction.BspTNI.results=Bio.Restriction.Restriction.BspTNI-class.html#results,Variable Bio.Restriction.Restriction.BspXI.results=Bio.Restriction.Restriction.BspXI-class.html#results,Variable Bio.Restriction.Restriction.BsrBI.results=Bio.Restriction.Restriction.BsrBI-class.html#results,Variable Bio.Restriction.Restriction.BsrDI.results=Bio.Restriction.Restriction.BsrDI-class.html#results,Variable Bio.Restriction.Restriction.BsrFI.results=Bio.Restriction.Restriction.BsrFI-class.html#results,Variable Bio.Restriction.Restriction.BsrGI.results=Bio.Restriction.Restriction.BsrGI-class.html#results,Variable Bio.Restriction.Restriction.BsrI.results=Bio.Restriction.Restriction.BsrI-class.html#results,Variable Bio.Restriction.Restriction.BsrSI.results=Bio.Restriction.Restriction.BsrSI-class.html#results,Variable Bio.Restriction.Restriction.BssAI.results=Bio.Restriction.Restriction.BssAI-class.html#results,Variable Bio.Restriction.Restriction.BssECI.results=Bio.Restriction.Restriction.BssECI-class.html#results,Variable Bio.Restriction.Restriction.BssHII.results=Bio.Restriction.Restriction.BssHII-class.html#results,Variable Bio.Restriction.Restriction.BssKI.results=Bio.Restriction.Restriction.BssKI-class.html#results,Variable Bio.Restriction.Restriction.BssMI.results=Bio.Restriction.Restriction.BssMI-class.html#results,Variable Bio.Restriction.Restriction.BssNAI.results=Bio.Restriction.Restriction.BssNAI-class.html#results,Variable Bio.Restriction.Restriction.BssNI.results=Bio.Restriction.Restriction.BssNI-class.html#results,Variable Bio.Restriction.Restriction.BssSI.results=Bio.Restriction.Restriction.BssSI-class.html#results,Variable Bio.Restriction.Restriction.BssT1I.results=Bio.Restriction.Restriction.BssT1I-class.html#results,Variable Bio.Restriction.Restriction.Bst1107I.results=Bio.Restriction.Restriction.Bst1107I-class.html#results,Variable Bio.Restriction.Restriction.Bst2BI.results=Bio.Restriction.Restriction.Bst2BI-class.html#results,Variable Bio.Restriction.Restriction.Bst2UI.results=Bio.Restriction.Restriction.Bst2UI-class.html#results,Variable Bio.Restriction.Restriction.Bst4CI.results=Bio.Restriction.Restriction.Bst4CI-class.html#results,Variable Bio.Restriction.Restriction.Bst6I.results=Bio.Restriction.Restriction.Bst6I-class.html#results,Variable Bio.Restriction.Restriction.Bst98I.results=Bio.Restriction.Restriction.Bst98I-class.html#results,Variable Bio.Restriction.Restriction.BstACI.results=Bio.Restriction.Restriction.BstACI-class.html#results,Variable Bio.Restriction.Restriction.BstAFI.results=Bio.Restriction.Restriction.BstAFI-class.html#results,Variable Bio.Restriction.Restriction.BstAPI.results=Bio.Restriction.Restriction.BstAPI-class.html#results,Variable Bio.Restriction.Restriction.BstAUI.results=Bio.Restriction.Restriction.BstAUI-class.html#results,Variable Bio.Restriction.Restriction.BstBAI.results=Bio.Restriction.Restriction.BstBAI-class.html#results,Variable Bio.Restriction.Restriction.BstBI.results=Bio.Restriction.Restriction.BstBI-class.html#results,Variable Bio.Restriction.Restriction.BstC8I.results=Bio.Restriction.Restriction.BstC8I-class.html#results,Variable Bio.Restriction.Restriction.BstDEI.results=Bio.Restriction.Restriction.BstDEI-class.html#results,Variable Bio.Restriction.Restriction.BstDSI.results=Bio.Restriction.Restriction.BstDSI-class.html#results,Variable Bio.Restriction.Restriction.BstEII.results=Bio.Restriction.Restriction.BstEII-class.html#results,Variable Bio.Restriction.Restriction.BstENI.results=Bio.Restriction.Restriction.BstENI-class.html#results,Variable Bio.Restriction.Restriction.BstF5I.results=Bio.Restriction.Restriction.BstF5I-class.html#results,Variable Bio.Restriction.Restriction.BstFNI.results=Bio.Restriction.Restriction.BstFNI-class.html#results,Variable Bio.Restriction.Restriction.BstH2I.results=Bio.Restriction.Restriction.BstH2I-class.html#results,Variable Bio.Restriction.Restriction.BstHHI.results=Bio.Restriction.Restriction.BstHHI-class.html#results,Variable Bio.Restriction.Restriction.BstKTI.results=Bio.Restriction.Restriction.BstKTI-class.html#results,Variable Bio.Restriction.Restriction.BstMAI.results=Bio.Restriction.Restriction.BstMAI-class.html#results,Variable Bio.Restriction.Restriction.BstMBI.results=Bio.Restriction.Restriction.BstMBI-class.html#results,Variable Bio.Restriction.Restriction.BstMCI.results=Bio.Restriction.Restriction.BstMCI-class.html#results,Variable Bio.Restriction.Restriction.BstMWI.results=Bio.Restriction.Restriction.BstMWI-class.html#results,Variable Bio.Restriction.Restriction.BstNI.results=Bio.Restriction.Restriction.BstNI-class.html#results,Variable Bio.Restriction.Restriction.BstNSI.results=Bio.Restriction.Restriction.BstNSI-class.html#results,Variable Bio.Restriction.Restriction.BstOI.results=Bio.Restriction.Restriction.BstOI-class.html#results,Variable Bio.Restriction.Restriction.BstPAI.results=Bio.Restriction.Restriction.BstPAI-class.html#results,Variable Bio.Restriction.Restriction.BstPI.results=Bio.Restriction.Restriction.BstPI-class.html#results,Variable Bio.Restriction.Restriction.BstSCI.results=Bio.Restriction.Restriction.BstSCI-class.html#results,Variable Bio.Restriction.Restriction.BstSFI.results=Bio.Restriction.Restriction.BstSFI-class.html#results,Variable Bio.Restriction.Restriction.BstSLI.results=Bio.Restriction.Restriction.BstSLI-class.html#results,Variable Bio.Restriction.Restriction.BstSNI.results=Bio.Restriction.Restriction.BstSNI-class.html#results,Variable Bio.Restriction.Restriction.BstUI.results=Bio.Restriction.Restriction.BstUI-class.html#results,Variable Bio.Restriction.Restriction.BstV1I.results=Bio.Restriction.Restriction.BstV1I-class.html#results,Variable Bio.Restriction.Restriction.BstV2I.results=Bio.Restriction.Restriction.BstV2I-class.html#results,Variable Bio.Restriction.Restriction.BstX2I.results=Bio.Restriction.Restriction.BstX2I-class.html#results,Variable Bio.Restriction.Restriction.BstXI.results=Bio.Restriction.Restriction.BstXI-class.html#results,Variable Bio.Restriction.Restriction.BstYI.results=Bio.Restriction.Restriction.BstYI-class.html#results,Variable Bio.Restriction.Restriction.BstZ17I.results=Bio.Restriction.Restriction.BstZ17I-class.html#results,Variable Bio.Restriction.Restriction.BstZI.results=Bio.Restriction.Restriction.BstZI-class.html#results,Variable Bio.Restriction.Restriction.Bsu15I.results=Bio.Restriction.Restriction.Bsu15I-class.html#results,Variable Bio.Restriction.Restriction.Bsu36I.results=Bio.Restriction.Restriction.Bsu36I-class.html#results,Variable Bio.Restriction.Restriction.BsuRI.results=Bio.Restriction.Restriction.BsuRI-class.html#results,Variable Bio.Restriction.Restriction.BsuTUI.results=Bio.Restriction.Restriction.BsuTUI-class.html#results,Variable Bio.Restriction.Restriction.BtgI.results=Bio.Restriction.Restriction.BtgI-class.html#results,Variable Bio.Restriction.Restriction.BtgZI.results=Bio.Restriction.Restriction.BtgZI-class.html#results,Variable Bio.Restriction.Restriction.BthCI.results=Bio.Restriction.Restriction.BthCI-class.html#results,Variable Bio.Restriction.Restriction.BtrI.results=Bio.Restriction.Restriction.BtrI-class.html#results,Variable Bio.Restriction.Restriction.BtsCI.results=Bio.Restriction.Restriction.BtsCI-class.html#results,Variable Bio.Restriction.Restriction.BtsI.results=Bio.Restriction.Restriction.BtsI-class.html#results,Variable Bio.Restriction.Restriction.BtuMI.results=Bio.Restriction.Restriction.BtuMI-class.html#results,Variable Bio.Restriction.Restriction.BveI.results=Bio.Restriction.Restriction.BveI-class.html#results,Variable Bio.Restriction.Restriction.Cac8I.results=Bio.Restriction.Restriction.Cac8I-class.html#results,Variable Bio.Restriction.Restriction.CaiI.results=Bio.Restriction.Restriction.CaiI-class.html#results,Variable Bio.Restriction.Restriction.CauII.results=Bio.Restriction.Restriction.CauII-class.html#results,Variable Bio.Restriction.Restriction.CciI.results=Bio.Restriction.Restriction.CciI-class.html#results,Variable Bio.Restriction.Restriction.CciNI.results=Bio.Restriction.Restriction.CciNI-class.html#results,Variable Bio.Restriction.Restriction.CdiI.results=Bio.Restriction.Restriction.CdiI-class.html#results,Variable Bio.Restriction.Restriction.CdpI.results=Bio.Restriction.Restriction.CdpI-class.html#results,Variable Bio.Restriction.Restriction.CelII.results=Bio.Restriction.Restriction.CelII-class.html#results,Variable Bio.Restriction.Restriction.CfoI.results=Bio.Restriction.Restriction.CfoI-class.html#results,Variable Bio.Restriction.Restriction.Cfr10I.results=Bio.Restriction.Restriction.Cfr10I-class.html#results,Variable Bio.Restriction.Restriction.Cfr13I.results=Bio.Restriction.Restriction.Cfr13I-class.html#results,Variable Bio.Restriction.Restriction.Cfr42I.results=Bio.Restriction.Restriction.Cfr42I-class.html#results,Variable Bio.Restriction.Restriction.Cfr9I.results=Bio.Restriction.Restriction.Cfr9I-class.html#results,Variable Bio.Restriction.Restriction.CfrI.results=Bio.Restriction.Restriction.CfrI-class.html#results,Variable Bio.Restriction.Restriction.ChaI.results=Bio.Restriction.Restriction.ChaI-class.html#results,Variable Bio.Restriction.Restriction.CjeI.results=Bio.Restriction.Restriction.CjeI-class.html#results,Variable Bio.Restriction.Restriction.CjeNII.results=Bio.Restriction.Restriction.CjeNII-class.html#results,Variable Bio.Restriction.Restriction.CjePI.results=Bio.Restriction.Restriction.CjePI-class.html#results,Variable Bio.Restriction.Restriction.CjuI.results=Bio.Restriction.Restriction.CjuI-class.html#results,Variable Bio.Restriction.Restriction.CjuII.results=Bio.Restriction.Restriction.CjuII-class.html#results,Variable Bio.Restriction.Restriction.ClaI.results=Bio.Restriction.Restriction.ClaI-class.html#results,Variable Bio.Restriction.Restriction.CpoI.results=Bio.Restriction.Restriction.CpoI-class.html#results,Variable Bio.Restriction.Restriction.CseI.results=Bio.Restriction.Restriction.CseI-class.html#results,Variable Bio.Restriction.Restriction.CsiI.results=Bio.Restriction.Restriction.CsiI-class.html#results,Variable Bio.Restriction.Restriction.Csp45I.results=Bio.Restriction.Restriction.Csp45I-class.html#results,Variable Bio.Restriction.Restriction.Csp6I.results=Bio.Restriction.Restriction.Csp6I-class.html#results,Variable Bio.Restriction.Restriction.CspAI.results=Bio.Restriction.Restriction.CspAI-class.html#results,Variable Bio.Restriction.Restriction.CspCI.results=Bio.Restriction.Restriction.CspCI-class.html#results,Variable Bio.Restriction.Restriction.CspI.results=Bio.Restriction.Restriction.CspI-class.html#results,Variable Bio.Restriction.Restriction.CstMI.results=Bio.Restriction.Restriction.CstMI-class.html#results,Variable Bio.Restriction.Restriction.CviAII.results=Bio.Restriction.Restriction.CviAII-class.html#results,Variable Bio.Restriction.Restriction.CviJI.results=Bio.Restriction.Restriction.CviJI-class.html#results,Variable Bio.Restriction.Restriction.CviKI_1.results=Bio.Restriction.Restriction.CviKI_1-class.html#results,Variable Bio.Restriction.Restriction.CviQI.results=Bio.Restriction.Restriction.CviQI-class.html#results,Variable Bio.Restriction.Restriction.CviRI.results=Bio.Restriction.Restriction.CviRI-class.html#results,Variable Bio.Restriction.Restriction.DdeI.results=Bio.Restriction.Restriction.DdeI-class.html#results,Variable Bio.Restriction.Restriction.DinI.results=Bio.Restriction.Restriction.DinI-class.html#results,Variable Bio.Restriction.Restriction.DpnI.results=Bio.Restriction.Restriction.DpnI-class.html#results,Variable Bio.Restriction.Restriction.DpnII.results=Bio.Restriction.Restriction.DpnII-class.html#results,Variable Bio.Restriction.Restriction.DraI.results=Bio.Restriction.Restriction.DraI-class.html#results,Variable Bio.Restriction.Restriction.DraII.results=Bio.Restriction.Restriction.DraII-class.html#results,Variable Bio.Restriction.Restriction.DraIII.results=Bio.Restriction.Restriction.DraIII-class.html#results,Variable Bio.Restriction.Restriction.DraRI.results=Bio.Restriction.Restriction.DraRI-class.html#results,Variable Bio.Restriction.Restriction.DrdI.results=Bio.Restriction.Restriction.DrdI-class.html#results,Variable Bio.Restriction.Restriction.DrdII.results=Bio.Restriction.Restriction.DrdII-class.html#results,Variable Bio.Restriction.Restriction.DrdIV.results=Bio.Restriction.Restriction.DrdIV-class.html#results,Variable Bio.Restriction.Restriction.DriI.results=Bio.Restriction.Restriction.DriI-class.html#results,Variable Bio.Restriction.Restriction.DsaI.results=Bio.Restriction.Restriction.DsaI-class.html#results,Variable Bio.Restriction.Restriction.DseDI.results=Bio.Restriction.Restriction.DseDI-class.html#results,Variable Bio.Restriction.Restriction.EaeI.results=Bio.Restriction.Restriction.EaeI-class.html#results,Variable Bio.Restriction.Restriction.EagI.results=Bio.Restriction.Restriction.EagI-class.html#results,Variable Bio.Restriction.Restriction.Eam1104I.results=Bio.Restriction.Restriction.Eam1104I-class.html#results,Variable Bio.Restriction.Restriction.Eam1105I.results=Bio.Restriction.Restriction.Eam1105I-class.html#results,Variable Bio.Restriction.Restriction.EarI.results=Bio.Restriction.Restriction.EarI-class.html#results,Variable Bio.Restriction.Restriction.EciI.results=Bio.Restriction.Restriction.EciI-class.html#results,Variable Bio.Restriction.Restriction.Ecl136II.results=Bio.Restriction.Restriction.Ecl136II-class.html#results,Variable Bio.Restriction.Restriction.EclXI.results=Bio.Restriction.Restriction.EclXI-class.html#results,Variable Bio.Restriction.Restriction.Eco105I.results=Bio.Restriction.Restriction.Eco105I-class.html#results,Variable Bio.Restriction.Restriction.Eco130I.results=Bio.Restriction.Restriction.Eco130I-class.html#results,Variable Bio.Restriction.Restriction.Eco147I.results=Bio.Restriction.Restriction.Eco147I-class.html#results,Variable Bio.Restriction.Restriction.Eco24I.results=Bio.Restriction.Restriction.Eco24I-class.html#results,Variable Bio.Restriction.Restriction.Eco31I.results=Bio.Restriction.Restriction.Eco31I-class.html#results,Variable Bio.Restriction.Restriction.Eco32I.results=Bio.Restriction.Restriction.Eco32I-class.html#results,Variable Bio.Restriction.Restriction.Eco47I.results=Bio.Restriction.Restriction.Eco47I-class.html#results,Variable Bio.Restriction.Restriction.Eco47III.results=Bio.Restriction.Restriction.Eco47III-class.html#results,Variable Bio.Restriction.Restriction.Eco52I.results=Bio.Restriction.Restriction.Eco52I-class.html#results,Variable Bio.Restriction.Restriction.Eco53kI.results=Bio.Restriction.Restriction.Eco53kI-class.html#results,Variable Bio.Restriction.Restriction.Eco57I.results=Bio.Restriction.Restriction.Eco57I-class.html#results,Variable Bio.Restriction.Restriction.Eco57MI.results=Bio.Restriction.Restriction.Eco57MI-class.html#results,Variable Bio.Restriction.Restriction.Eco72I.results=Bio.Restriction.Restriction.Eco72I-class.html#results,Variable Bio.Restriction.Restriction.Eco81I.results=Bio.Restriction.Restriction.Eco81I-class.html#results,Variable Bio.Restriction.Restriction.Eco88I.results=Bio.Restriction.Restriction.Eco88I-class.html#results,Variable Bio.Restriction.Restriction.Eco91I.results=Bio.Restriction.Restriction.Eco91I-class.html#results,Variable Bio.Restriction.Restriction.EcoHI.results=Bio.Restriction.Restriction.EcoHI-class.html#results,Variable Bio.Restriction.Restriction.EcoICRI.results=Bio.Restriction.Restriction.EcoICRI-class.html#results,Variable Bio.Restriction.Restriction.EcoNI.results=Bio.Restriction.Restriction.EcoNI-class.html#results,Variable Bio.Restriction.Restriction.EcoO109I.results=Bio.Restriction.Restriction.EcoO109I-class.html#results,Variable Bio.Restriction.Restriction.EcoO65I.results=Bio.Restriction.Restriction.EcoO65I-class.html#results,Variable Bio.Restriction.Restriction.EcoRI.results=Bio.Restriction.Restriction.EcoRI-class.html#results,Variable Bio.Restriction.Restriction.EcoRII.results=Bio.Restriction.Restriction.EcoRII-class.html#results,Variable Bio.Restriction.Restriction.EcoRV.results=Bio.Restriction.Restriction.EcoRV-class.html#results,Variable Bio.Restriction.Restriction.EcoT14I.results=Bio.Restriction.Restriction.EcoT14I-class.html#results,Variable Bio.Restriction.Restriction.EcoT22I.results=Bio.Restriction.Restriction.EcoT22I-class.html#results,Variable Bio.Restriction.Restriction.EcoT38I.results=Bio.Restriction.Restriction.EcoT38I-class.html#results,Variable Bio.Restriction.Restriction.EgeI.results=Bio.Restriction.Restriction.EgeI-class.html#results,Variable Bio.Restriction.Restriction.EheI.results=Bio.Restriction.Restriction.EheI-class.html#results,Variable Bio.Restriction.Restriction.ErhI.results=Bio.Restriction.Restriction.ErhI-class.html#results,Variable Bio.Restriction.Restriction.EsaBC3I.results=Bio.Restriction.Restriction.EsaBC3I-class.html#results,Variable Bio.Restriction.Restriction.EsaSSI.results=Bio.Restriction.Restriction.EsaSSI-class.html#results,Variable Bio.Restriction.Restriction.Esp3I.results=Bio.Restriction.Restriction.Esp3I-class.html#results,Variable Bio.Restriction.Restriction.EspI.results=Bio.Restriction.Restriction.EspI-class.html#results,Variable Bio.Restriction.Restriction.FaeI.results=Bio.Restriction.Restriction.FaeI-class.html#results,Variable Bio.Restriction.Restriction.FaiI.results=Bio.Restriction.Restriction.FaiI-class.html#results,Variable Bio.Restriction.Restriction.FalI.results=Bio.Restriction.Restriction.FalI-class.html#results,Variable Bio.Restriction.Restriction.FaqI.results=Bio.Restriction.Restriction.FaqI-class.html#results,Variable Bio.Restriction.Restriction.FatI.results=Bio.Restriction.Restriction.FatI-class.html#results,Variable Bio.Restriction.Restriction.FauI.results=Bio.Restriction.Restriction.FauI-class.html#results,Variable Bio.Restriction.Restriction.FauNDI.results=Bio.Restriction.Restriction.FauNDI-class.html#results,Variable Bio.Restriction.Restriction.FbaI.results=Bio.Restriction.Restriction.FbaI-class.html#results,Variable Bio.Restriction.Restriction.FblI.results=Bio.Restriction.Restriction.FblI-class.html#results,Variable Bio.Restriction.Restriction.FinI.results=Bio.Restriction.Restriction.FinI-class.html#results,Variable Bio.Restriction.Restriction.FmuI.results=Bio.Restriction.Restriction.FmuI-class.html#results,Variable Bio.Restriction.Restriction.Fnu4HI.results=Bio.Restriction.Restriction.Fnu4HI-class.html#results,Variable Bio.Restriction.Restriction.FnuDII.results=Bio.Restriction.Restriction.FnuDII-class.html#results,Variable Bio.Restriction.Restriction.FokI.results=Bio.Restriction.Restriction.FokI-class.html#results,Variable Bio.Restriction.Restriction.FriOI.results=Bio.Restriction.Restriction.FriOI-class.html#results,Variable Bio.Restriction.Restriction.FseI.results=Bio.Restriction.Restriction.FseI-class.html#results,Variable Bio.Restriction.Restriction.Fsp4HI.results=Bio.Restriction.Restriction.Fsp4HI-class.html#results,Variable Bio.Restriction.Restriction.FspAI.results=Bio.Restriction.Restriction.FspAI-class.html#results,Variable Bio.Restriction.Restriction.FspBI.results=Bio.Restriction.Restriction.FspBI-class.html#results,Variable Bio.Restriction.Restriction.FspI.results=Bio.Restriction.Restriction.FspI-class.html#results,Variable Bio.Restriction.Restriction.GdiII.results=Bio.Restriction.Restriction.GdiII-class.html#results,Variable Bio.Restriction.Restriction.GlaI.results=Bio.Restriction.Restriction.GlaI-class.html#results,Variable Bio.Restriction.Restriction.GluI.results=Bio.Restriction.Restriction.GluI-class.html#results,Variable Bio.Restriction.Restriction.GsaI.results=Bio.Restriction.Restriction.GsaI-class.html#results,Variable Bio.Restriction.Restriction.GsuI.results=Bio.Restriction.Restriction.GsuI-class.html#results,Variable Bio.Restriction.Restriction.HaeI.results=Bio.Restriction.Restriction.HaeI-class.html#results,Variable Bio.Restriction.Restriction.HaeII.results=Bio.Restriction.Restriction.HaeII-class.html#results,Variable Bio.Restriction.Restriction.HaeIII.results=Bio.Restriction.Restriction.HaeIII-class.html#results,Variable Bio.Restriction.Restriction.HapII.results=Bio.Restriction.Restriction.HapII-class.html#results,Variable Bio.Restriction.Restriction.HgaI.results=Bio.Restriction.Restriction.HgaI-class.html#results,Variable Bio.Restriction.Restriction.HgiAI.results=Bio.Restriction.Restriction.HgiAI-class.html#results,Variable Bio.Restriction.Restriction.HgiCI.results=Bio.Restriction.Restriction.HgiCI-class.html#results,Variable Bio.Restriction.Restriction.HgiEII.results=Bio.Restriction.Restriction.HgiEII-class.html#results,Variable Bio.Restriction.Restriction.HgiJII.results=Bio.Restriction.Restriction.HgiJII-class.html#results,Variable Bio.Restriction.Restriction.HhaI.results=Bio.Restriction.Restriction.HhaI-class.html#results,Variable Bio.Restriction.Restriction.Hin1I.results=Bio.Restriction.Restriction.Hin1I-class.html#results,Variable Bio.Restriction.Restriction.Hin1II.results=Bio.Restriction.Restriction.Hin1II-class.html#results,Variable Bio.Restriction.Restriction.Hin4I.results=Bio.Restriction.Restriction.Hin4I-class.html#results,Variable Bio.Restriction.Restriction.Hin4II.results=Bio.Restriction.Restriction.Hin4II-class.html#results,Variable Bio.Restriction.Restriction.Hin6I.results=Bio.Restriction.Restriction.Hin6I-class.html#results,Variable Bio.Restriction.Restriction.HinP1I.results=Bio.Restriction.Restriction.HinP1I-class.html#results,Variable Bio.Restriction.Restriction.HincII.results=Bio.Restriction.Restriction.HincII-class.html#results,Variable Bio.Restriction.Restriction.HindII.results=Bio.Restriction.Restriction.HindII-class.html#results,Variable Bio.Restriction.Restriction.HindIII.results=Bio.Restriction.Restriction.HindIII-class.html#results,Variable Bio.Restriction.Restriction.HinfI.results=Bio.Restriction.Restriction.HinfI-class.html#results,Variable Bio.Restriction.Restriction.HpaI.results=Bio.Restriction.Restriction.HpaI-class.html#results,Variable Bio.Restriction.Restriction.HpaII.results=Bio.Restriction.Restriction.HpaII-class.html#results,Variable Bio.Restriction.Restriction.HphI.results=Bio.Restriction.Restriction.HphI-class.html#results,Variable Bio.Restriction.Restriction.Hpy166II.results=Bio.Restriction.Restriction.Hpy166II-class.html#results,Variable Bio.Restriction.Restriction.Hpy178III.results=Bio.Restriction.Restriction.Hpy178III-class.html#results,Variable Bio.Restriction.Restriction.Hpy188I.results=Bio.Restriction.Restriction.Hpy188I-class.html#results,Variable Bio.Restriction.Restriction.Hpy188III.results=Bio.Restriction.Restriction.Hpy188III-class.html#results,Variable Bio.Restriction.Restriction.Hpy8I.results=Bio.Restriction.Restriction.Hpy8I-class.html#results,Variable Bio.Restriction.Restriction.Hpy99I.results=Bio.Restriction.Restriction.Hpy99I-class.html#results,Variable Bio.Restriction.Restriction.HpyAV.results=Bio.Restriction.Restriction.HpyAV-class.html#results,Variable Bio.Restriction.Restriction.HpyCH4III.results=Bio.Restriction.Restriction.HpyCH4III-class.html#results,Variable Bio.Restriction.Restriction.HpyCH4IV.results=Bio.Restriction.Restriction.HpyCH4IV-class.html#results,Variable Bio.Restriction.Restriction.HpyCH4V.results=Bio.Restriction.Restriction.HpyCH4V-class.html#results,Variable Bio.Restriction.Restriction.HpyF10VI.results=Bio.Restriction.Restriction.HpyF10VI-class.html#results,Variable Bio.Restriction.Restriction.HpyF3I.results=Bio.Restriction.Restriction.HpyF3I-class.html#results,Variable Bio.Restriction.Restriction.Hsp92I.results=Bio.Restriction.Restriction.Hsp92I-class.html#results,Variable Bio.Restriction.Restriction.Hsp92II.results=Bio.Restriction.Restriction.Hsp92II-class.html#results,Variable Bio.Restriction.Restriction.HspAI.results=Bio.Restriction.Restriction.HspAI-class.html#results,Variable Bio.Restriction.Restriction.ItaI.results=Bio.Restriction.Restriction.ItaI-class.html#results,Variable Bio.Restriction.Restriction.KasI.results=Bio.Restriction.Restriction.KasI-class.html#results,Variable Bio.Restriction.Restriction.KflI.results=Bio.Restriction.Restriction.KflI-class.html#results,Variable Bio.Restriction.Restriction.Kpn2I.results=Bio.Restriction.Restriction.Kpn2I-class.html#results,Variable Bio.Restriction.Restriction.KpnI.results=Bio.Restriction.Restriction.KpnI-class.html#results,Variable Bio.Restriction.Restriction.Ksp22I.results=Bio.Restriction.Restriction.Ksp22I-class.html#results,Variable Bio.Restriction.Restriction.Ksp632I.results=Bio.Restriction.Restriction.Ksp632I-class.html#results,Variable Bio.Restriction.Restriction.KspAI.results=Bio.Restriction.Restriction.KspAI-class.html#results,Variable Bio.Restriction.Restriction.KspI.results=Bio.Restriction.Restriction.KspI-class.html#results,Variable Bio.Restriction.Restriction.Kzo9I.results=Bio.Restriction.Restriction.Kzo9I-class.html#results,Variable Bio.Restriction.Restriction.LguI.results=Bio.Restriction.Restriction.LguI-class.html#results,Variable Bio.Restriction.Restriction.LpnI.results=Bio.Restriction.Restriction.LpnI-class.html#results,Variable Bio.Restriction.Restriction.Lsp1109I.results=Bio.Restriction.Restriction.Lsp1109I-class.html#results,Variable Bio.Restriction.Restriction.LweI.results=Bio.Restriction.Restriction.LweI-class.html#results,Variable Bio.Restriction.Restriction.MabI.results=Bio.Restriction.Restriction.MabI-class.html#results,Variable Bio.Restriction.Restriction.MaeI.results=Bio.Restriction.Restriction.MaeI-class.html#results,Variable Bio.Restriction.Restriction.MaeII.results=Bio.Restriction.Restriction.MaeII-class.html#results,Variable Bio.Restriction.Restriction.MaeIII.results=Bio.Restriction.Restriction.MaeIII-class.html#results,Variable Bio.Restriction.Restriction.MalI.results=Bio.Restriction.Restriction.MalI-class.html#results,Variable Bio.Restriction.Restriction.MaqI.results=Bio.Restriction.Restriction.MaqI-class.html#results,Variable Bio.Restriction.Restriction.MauBI.results=Bio.Restriction.Restriction.MauBI-class.html#results,Variable Bio.Restriction.Restriction.MbiI.results=Bio.Restriction.Restriction.MbiI-class.html#results,Variable Bio.Restriction.Restriction.MboI.results=Bio.Restriction.Restriction.MboI-class.html#results,Variable Bio.Restriction.Restriction.MboII.results=Bio.Restriction.Restriction.MboII-class.html#results,Variable Bio.Restriction.Restriction.McaTI.results=Bio.Restriction.Restriction.McaTI-class.html#results,Variable Bio.Restriction.Restriction.McrI.results=Bio.Restriction.Restriction.McrI-class.html#results,Variable Bio.Restriction.Restriction.MfeI.results=Bio.Restriction.Restriction.MfeI-class.html#results,Variable Bio.Restriction.Restriction.MflI.results=Bio.Restriction.Restriction.MflI-class.html#results,Variable Bio.Restriction.Restriction.MhlI.results=Bio.Restriction.Restriction.MhlI-class.html#results,Variable Bio.Restriction.Restriction.MjaIV.results=Bio.Restriction.Restriction.MjaIV-class.html#results,Variable Bio.Restriction.Restriction.MlsI.results=Bio.Restriction.Restriction.MlsI-class.html#results,Variable Bio.Restriction.Restriction.MluI.results=Bio.Restriction.Restriction.MluI-class.html#results,Variable Bio.Restriction.Restriction.MluNI.results=Bio.Restriction.Restriction.MluNI-class.html#results,Variable Bio.Restriction.Restriction.Mly113I.results=Bio.Restriction.Restriction.Mly113I-class.html#results,Variable Bio.Restriction.Restriction.MlyI.results=Bio.Restriction.Restriction.MlyI-class.html#results,Variable Bio.Restriction.Restriction.MmeI.results=Bio.Restriction.Restriction.MmeI-class.html#results,Variable Bio.Restriction.Restriction.MnlI.results=Bio.Restriction.Restriction.MnlI-class.html#results,Variable Bio.Restriction.Restriction.Mph1103I.results=Bio.Restriction.Restriction.Mph1103I-class.html#results,Variable Bio.Restriction.Restriction.MreI.results=Bio.Restriction.Restriction.MreI-class.html#results,Variable Bio.Restriction.Restriction.MroI.results=Bio.Restriction.Restriction.MroI-class.html#results,Variable Bio.Restriction.Restriction.MroNI.results=Bio.Restriction.Restriction.MroNI-class.html#results,Variable Bio.Restriction.Restriction.MroXI.results=Bio.Restriction.Restriction.MroXI-class.html#results,Variable Bio.Restriction.Restriction.MscI.results=Bio.Restriction.Restriction.MscI-class.html#results,Variable Bio.Restriction.Restriction.MseI.results=Bio.Restriction.Restriction.MseI-class.html#results,Variable Bio.Restriction.Restriction.MslI.results=Bio.Restriction.Restriction.MslI-class.html#results,Variable Bio.Restriction.Restriction.Msp20I.results=Bio.Restriction.Restriction.Msp20I-class.html#results,Variable Bio.Restriction.Restriction.MspA1I.results=Bio.Restriction.Restriction.MspA1I-class.html#results,Variable Bio.Restriction.Restriction.MspCI.results=Bio.Restriction.Restriction.MspCI-class.html#results,Variable Bio.Restriction.Restriction.MspI.results=Bio.Restriction.Restriction.MspI-class.html#results,Variable Bio.Restriction.Restriction.MspR9I.results=Bio.Restriction.Restriction.MspR9I-class.html#results,Variable Bio.Restriction.Restriction.MssI.results=Bio.Restriction.Restriction.MssI-class.html#results,Variable Bio.Restriction.Restriction.MstI.results=Bio.Restriction.Restriction.MstI-class.html#results,Variable Bio.Restriction.Restriction.MunI.results=Bio.Restriction.Restriction.MunI-class.html#results,Variable Bio.Restriction.Restriction.Mva1269I.results=Bio.Restriction.Restriction.Mva1269I-class.html#results,Variable Bio.Restriction.Restriction.MvaI.results=Bio.Restriction.Restriction.MvaI-class.html#results,Variable Bio.Restriction.Restriction.MvnI.results=Bio.Restriction.Restriction.MvnI-class.html#results,Variable Bio.Restriction.Restriction.MvrI.results=Bio.Restriction.Restriction.MvrI-class.html#results,Variable Bio.Restriction.Restriction.MwoI.results=Bio.Restriction.Restriction.MwoI-class.html#results,Variable Bio.Restriction.Restriction.NaeI.results=Bio.Restriction.Restriction.NaeI-class.html#results,Variable Bio.Restriction.Restriction.NarI.results=Bio.Restriction.Restriction.NarI-class.html#results,Variable Bio.Restriction.Restriction.NciI.results=Bio.Restriction.Restriction.NciI-class.html#results,Variable Bio.Restriction.Restriction.NcoI.results=Bio.Restriction.Restriction.NcoI-class.html#results,Variable Bio.Restriction.Restriction.NdeI.results=Bio.Restriction.Restriction.NdeI-class.html#results,Variable Bio.Restriction.Restriction.NdeII.results=Bio.Restriction.Restriction.NdeII-class.html#results,Variable Bio.Restriction.Restriction.NgoAVIII.results=Bio.Restriction.Restriction.NgoAVIII-class.html#results,Variable Bio.Restriction.Restriction.NgoMIV.results=Bio.Restriction.Restriction.NgoMIV-class.html#results,Variable Bio.Restriction.Restriction.NhaXI.results=Bio.Restriction.Restriction.NhaXI-class.html#results,Variable Bio.Restriction.Restriction.NheI.results=Bio.Restriction.Restriction.NheI-class.html#results,Variable Bio.Restriction.Restriction.NlaCI.results=Bio.Restriction.Restriction.NlaCI-class.html#results,Variable Bio.Restriction.Restriction.NlaIII.results=Bio.Restriction.Restriction.NlaIII-class.html#results,Variable Bio.Restriction.Restriction.NlaIV.results=Bio.Restriction.Restriction.NlaIV-class.html#results,Variable Bio.Restriction.Restriction.Nli3877I.results=Bio.Restriction.Restriction.Nli3877I-class.html#results,Variable Bio.Restriction.Restriction.NmeAIII.results=Bio.Restriction.Restriction.NmeAIII-class.html#results,Variable Bio.Restriction.Restriction.NmeDI.results=Bio.Restriction.Restriction.NmeDI-class.html#results,Variable Bio.Restriction.Restriction.NmuCI.results=Bio.Restriction.Restriction.NmuCI-class.html#results,Variable Bio.Restriction.Restriction.NotI.results=Bio.Restriction.Restriction.NotI-class.html#results,Variable Bio.Restriction.Restriction.NruI.results=Bio.Restriction.Restriction.NruI-class.html#results,Variable Bio.Restriction.Restriction.NsbI.results=Bio.Restriction.Restriction.NsbI-class.html#results,Variable Bio.Restriction.Restriction.NsiI.results=Bio.Restriction.Restriction.NsiI-class.html#results,Variable Bio.Restriction.Restriction.NspBII.results=Bio.Restriction.Restriction.NspBII-class.html#results,Variable Bio.Restriction.Restriction.NspI.results=Bio.Restriction.Restriction.NspI-class.html#results,Variable Bio.Restriction.Restriction.NspV.results=Bio.Restriction.Restriction.NspV-class.html#results,Variable Bio.Restriction.Restriction.OliI.results=Bio.Restriction.Restriction.OliI-class.html#results,Variable Bio.Restriction.Restriction.PabI.results=Bio.Restriction.Restriction.PabI-class.html#results,Variable Bio.Restriction.Restriction.PacI.results=Bio.Restriction.Restriction.PacI-class.html#results,Variable Bio.Restriction.Restriction.PaeI.results=Bio.Restriction.Restriction.PaeI-class.html#results,Variable Bio.Restriction.Restriction.PaeR7I.results=Bio.Restriction.Restriction.PaeR7I-class.html#results,Variable Bio.Restriction.Restriction.PagI.results=Bio.Restriction.Restriction.PagI-class.html#results,Variable Bio.Restriction.Restriction.PalAI.results=Bio.Restriction.Restriction.PalAI-class.html#results,Variable Bio.Restriction.Restriction.PasI.results=Bio.Restriction.Restriction.PasI-class.html#results,Variable Bio.Restriction.Restriction.PauI.results=Bio.Restriction.Restriction.PauI-class.html#results,Variable Bio.Restriction.Restriction.PceI.results=Bio.Restriction.Restriction.PceI-class.html#results,Variable Bio.Restriction.Restriction.PciI.results=Bio.Restriction.Restriction.PciI-class.html#results,Variable Bio.Restriction.Restriction.PciSI.results=Bio.Restriction.Restriction.PciSI-class.html#results,Variable Bio.Restriction.Restriction.PctI.results=Bio.Restriction.Restriction.PctI-class.html#results,Variable Bio.Restriction.Restriction.PdiI.results=Bio.Restriction.Restriction.PdiI-class.html#results,Variable Bio.Restriction.Restriction.PdmI.results=Bio.Restriction.Restriction.PdmI-class.html#results,Variable Bio.Restriction.Restriction.PfeI.results=Bio.Restriction.Restriction.PfeI-class.html#results,Variable Bio.Restriction.Restriction.Pfl1108I.results=Bio.Restriction.Restriction.Pfl1108I-class.html#results,Variable Bio.Restriction.Restriction.Pfl23II.results=Bio.Restriction.Restriction.Pfl23II-class.html#results,Variable Bio.Restriction.Restriction.PflFI.results=Bio.Restriction.Restriction.PflFI-class.html#results,Variable Bio.Restriction.Restriction.PflMI.results=Bio.Restriction.Restriction.PflMI-class.html#results,Variable Bio.Restriction.Restriction.PfoI.results=Bio.Restriction.Restriction.PfoI-class.html#results,Variable Bio.Restriction.Restriction.PhoI.results=Bio.Restriction.Restriction.PhoI-class.html#results,Variable Bio.Restriction.Restriction.PinAI.results=Bio.Restriction.Restriction.PinAI-class.html#results,Variable Bio.Restriction.Restriction.PlaDI.results=Bio.Restriction.Restriction.PlaDI-class.html#results,Variable Bio.Restriction.Restriction.Ple19I.results=Bio.Restriction.Restriction.Ple19I-class.html#results,Variable Bio.Restriction.Restriction.PleI.results=Bio.Restriction.Restriction.PleI-class.html#results,Variable Bio.Restriction.Restriction.PmaCI.results=Bio.Restriction.Restriction.PmaCI-class.html#results,Variable Bio.Restriction.Restriction.PmeI.results=Bio.Restriction.Restriction.PmeI-class.html#results,Variable Bio.Restriction.Restriction.PmlI.results=Bio.Restriction.Restriction.PmlI-class.html#results,Variable Bio.Restriction.Restriction.PpiI.results=Bio.Restriction.Restriction.PpiI-class.html#results,Variable Bio.Restriction.Restriction.PpsI.results=Bio.Restriction.Restriction.PpsI-class.html#results,Variable Bio.Restriction.Restriction.Ppu10I.results=Bio.Restriction.Restriction.Ppu10I-class.html#results,Variable Bio.Restriction.Restriction.Ppu21I.results=Bio.Restriction.Restriction.Ppu21I-class.html#results,Variable Bio.Restriction.Restriction.PpuMI.results=Bio.Restriction.Restriction.PpuMI-class.html#results,Variable Bio.Restriction.Restriction.PscI.results=Bio.Restriction.Restriction.PscI-class.html#results,Variable Bio.Restriction.Restriction.PshAI.results=Bio.Restriction.Restriction.PshAI-class.html#results,Variable Bio.Restriction.Restriction.PshBI.results=Bio.Restriction.Restriction.PshBI-class.html#results,Variable Bio.Restriction.Restriction.PsiI.results=Bio.Restriction.Restriction.PsiI-class.html#results,Variable Bio.Restriction.Restriction.Psp03I.results=Bio.Restriction.Restriction.Psp03I-class.html#results,Variable Bio.Restriction.Restriction.Psp124BI.results=Bio.Restriction.Restriction.Psp124BI-class.html#results,Variable Bio.Restriction.Restriction.Psp1406I.results=Bio.Restriction.Restriction.Psp1406I-class.html#results,Variable Bio.Restriction.Restriction.Psp5II.results=Bio.Restriction.Restriction.Psp5II-class.html#results,Variable Bio.Restriction.Restriction.Psp6I.results=Bio.Restriction.Restriction.Psp6I-class.html#results,Variable Bio.Restriction.Restriction.PspCI.results=Bio.Restriction.Restriction.PspCI-class.html#results,Variable Bio.Restriction.Restriction.PspEI.results=Bio.Restriction.Restriction.PspEI-class.html#results,Variable Bio.Restriction.Restriction.PspGI.results=Bio.Restriction.Restriction.PspGI-class.html#results,Variable Bio.Restriction.Restriction.PspLI.results=Bio.Restriction.Restriction.PspLI-class.html#results,Variable Bio.Restriction.Restriction.PspN4I.results=Bio.Restriction.Restriction.PspN4I-class.html#results,Variable Bio.Restriction.Restriction.PspOMI.results=Bio.Restriction.Restriction.PspOMI-class.html#results,Variable Bio.Restriction.Restriction.PspOMII.results=Bio.Restriction.Restriction.PspOMII-class.html#results,Variable Bio.Restriction.Restriction.PspPI.results=Bio.Restriction.Restriction.PspPI-class.html#results,Variable Bio.Restriction.Restriction.PspPPI.results=Bio.Restriction.Restriction.PspPPI-class.html#results,Variable Bio.Restriction.Restriction.PspPRI.results=Bio.Restriction.Restriction.PspPRI-class.html#results,Variable Bio.Restriction.Restriction.PspXI.results=Bio.Restriction.Restriction.PspXI-class.html#results,Variable Bio.Restriction.Restriction.PsrI.results=Bio.Restriction.Restriction.PsrI-class.html#results,Variable Bio.Restriction.Restriction.PssI.results=Bio.Restriction.Restriction.PssI-class.html#results,Variable Bio.Restriction.Restriction.PstI.results=Bio.Restriction.Restriction.PstI-class.html#results,Variable Bio.Restriction.Restriction.PsuI.results=Bio.Restriction.Restriction.PsuI-class.html#results,Variable Bio.Restriction.Restriction.PsyI.results=Bio.Restriction.Restriction.PsyI-class.html#results,Variable Bio.Restriction.Restriction.PteI.results=Bio.Restriction.Restriction.PteI-class.html#results,Variable Bio.Restriction.Restriction.PvuI.results=Bio.Restriction.Restriction.PvuI-class.html#results,Variable Bio.Restriction.Restriction.PvuII.results=Bio.Restriction.Restriction.PvuII-class.html#results,Variable Bio.Restriction.Restriction.RcaI.results=Bio.Restriction.Restriction.RcaI-class.html#results,Variable Bio.Restriction.Restriction.RceI.results=Bio.Restriction.Restriction.RceI-class.html#results,Variable Bio.Restriction.Restriction.RgaI.results=Bio.Restriction.Restriction.RgaI-class.html#results,Variable Bio.Restriction.Restriction.RigI.results=Bio.Restriction.Restriction.RigI-class.html#results,Variable Bio.Restriction.Restriction.RleAI.results=Bio.Restriction.Restriction.RleAI-class.html#results,Variable Bio.Restriction.Restriction.RpaB5I.results=Bio.Restriction.Restriction.RpaB5I-class.html#results,Variable Bio.Restriction.Restriction.RruI.results=Bio.Restriction.Restriction.RruI-class.html#results,Variable Bio.Restriction.Restriction.RsaI.results=Bio.Restriction.Restriction.RsaI-class.html#results,Variable Bio.Restriction.Restriction.RsaNI.results=Bio.Restriction.Restriction.RsaNI-class.html#results,Variable Bio.Restriction.Restriction.RseI.results=Bio.Restriction.Restriction.RseI-class.html#results,Variable Bio.Restriction.Restriction.Rsr2I.results=Bio.Restriction.Restriction.Rsr2I-class.html#results,Variable Bio.Restriction.Restriction.RsrII.results=Bio.Restriction.Restriction.RsrII-class.html#results,Variable Bio.Restriction.Restriction.SacI.results=Bio.Restriction.Restriction.SacI-class.html#results,Variable Bio.Restriction.Restriction.SacII.results=Bio.Restriction.Restriction.SacII-class.html#results,Variable Bio.Restriction.Restriction.SalI.results=Bio.Restriction.Restriction.SalI-class.html#results,Variable Bio.Restriction.Restriction.SanDI.results=Bio.Restriction.Restriction.SanDI-class.html#results,Variable Bio.Restriction.Restriction.SapI.results=Bio.Restriction.Restriction.SapI-class.html#results,Variable Bio.Restriction.Restriction.SaqAI.results=Bio.Restriction.Restriction.SaqAI-class.html#results,Variable Bio.Restriction.Restriction.SatI.results=Bio.Restriction.Restriction.SatI-class.html#results,Variable Bio.Restriction.Restriction.Sau3AI.results=Bio.Restriction.Restriction.Sau3AI-class.html#results,Variable Bio.Restriction.Restriction.Sau96I.results=Bio.Restriction.Restriction.Sau96I-class.html#results,Variable Bio.Restriction.Restriction.SauI.results=Bio.Restriction.Restriction.SauI-class.html#results,Variable Bio.Restriction.Restriction.SbfI.results=Bio.Restriction.Restriction.SbfI-class.html#results,Variable Bio.Restriction.Restriction.ScaI.results=Bio.Restriction.Restriction.ScaI-class.html#results,Variable Bio.Restriction.Restriction.SchI.results=Bio.Restriction.Restriction.SchI-class.html#results,Variable Bio.Restriction.Restriction.SciI.results=Bio.Restriction.Restriction.SciI-class.html#results,Variable Bio.Restriction.Restriction.ScrFI.results=Bio.Restriction.Restriction.ScrFI-class.html#results,Variable Bio.Restriction.Restriction.SdaI.results=Bio.Restriction.Restriction.SdaI-class.html#results,Variable Bio.Restriction.Restriction.SdeAI.results=Bio.Restriction.Restriction.SdeAI-class.html#results,Variable Bio.Restriction.Restriction.SdeOSI.results=Bio.Restriction.Restriction.SdeOSI-class.html#results,Variable Bio.Restriction.Restriction.SduI.results=Bio.Restriction.Restriction.SduI-class.html#results,Variable Bio.Restriction.Restriction.SecI.results=Bio.Restriction.Restriction.SecI-class.html#results,Variable Bio.Restriction.Restriction.SelI.results=Bio.Restriction.Restriction.SelI-class.html#results,Variable Bio.Restriction.Restriction.SetI.results=Bio.Restriction.Restriction.SetI-class.html#results,Variable Bio.Restriction.Restriction.SexAI.results=Bio.Restriction.Restriction.SexAI-class.html#results,Variable Bio.Restriction.Restriction.SfaAI.results=Bio.Restriction.Restriction.SfaAI-class.html#results,Variable Bio.Restriction.Restriction.SfaNI.results=Bio.Restriction.Restriction.SfaNI-class.html#results,Variable Bio.Restriction.Restriction.SfcI.results=Bio.Restriction.Restriction.SfcI-class.html#results,Variable Bio.Restriction.Restriction.SfeI.results=Bio.Restriction.Restriction.SfeI-class.html#results,Variable Bio.Restriction.Restriction.SfiI.results=Bio.Restriction.Restriction.SfiI-class.html#results,Variable Bio.Restriction.Restriction.SfoI.results=Bio.Restriction.Restriction.SfoI-class.html#results,Variable Bio.Restriction.Restriction.Sfr274I.results=Bio.Restriction.Restriction.Sfr274I-class.html#results,Variable Bio.Restriction.Restriction.Sfr303I.results=Bio.Restriction.Restriction.Sfr303I-class.html#results,Variable Bio.Restriction.Restriction.SfuI.results=Bio.Restriction.Restriction.SfuI-class.html#results,Variable Bio.Restriction.Restriction.SgfI.results=Bio.Restriction.Restriction.SgfI-class.html#results,Variable Bio.Restriction.Restriction.SgrAI.results=Bio.Restriction.Restriction.SgrAI-class.html#results,Variable Bio.Restriction.Restriction.SgrBI.results=Bio.Restriction.Restriction.SgrBI-class.html#results,Variable Bio.Restriction.Restriction.SgrDI.results=Bio.Restriction.Restriction.SgrDI-class.html#results,Variable Bio.Restriction.Restriction.SgsI.results=Bio.Restriction.Restriction.SgsI-class.html#results,Variable Bio.Restriction.Restriction.SimI.results=Bio.Restriction.Restriction.SimI-class.html#results,Variable Bio.Restriction.Restriction.SinI.results=Bio.Restriction.Restriction.SinI-class.html#results,Variable Bio.Restriction.Restriction.SlaI.results=Bio.Restriction.Restriction.SlaI-class.html#results,Variable Bio.Restriction.Restriction.SmaI.results=Bio.Restriction.Restriction.SmaI-class.html#results,Variable Bio.Restriction.Restriction.SmiI.results=Bio.Restriction.Restriction.SmiI-class.html#results,Variable Bio.Restriction.Restriction.SmiMI.results=Bio.Restriction.Restriction.SmiMI-class.html#results,Variable Bio.Restriction.Restriction.SmlI.results=Bio.Restriction.Restriction.SmlI-class.html#results,Variable Bio.Restriction.Restriction.SmoI.results=Bio.Restriction.Restriction.SmoI-class.html#results,Variable Bio.Restriction.Restriction.SmuI.results=Bio.Restriction.Restriction.SmuI-class.html#results,Variable Bio.Restriction.Restriction.SnaBI.results=Bio.Restriction.Restriction.SnaBI-class.html#results,Variable Bio.Restriction.Restriction.SnaI.results=Bio.Restriction.Restriction.SnaI-class.html#results,Variable Bio.Restriction.Restriction.SpeI.results=Bio.Restriction.Restriction.SpeI-class.html#results,Variable Bio.Restriction.Restriction.SphI.results=Bio.Restriction.Restriction.SphI-class.html#results,Variable Bio.Restriction.Restriction.SplI.results=Bio.Restriction.Restriction.SplI-class.html#results,Variable Bio.Restriction.Restriction.SpoDI.results=Bio.Restriction.Restriction.SpoDI-class.html#results,Variable Bio.Restriction.Restriction.SrfI.results=Bio.Restriction.Restriction.SrfI-class.html#results,Variable Bio.Restriction.Restriction.Sse232I.results=Bio.Restriction.Restriction.Sse232I-class.html#results,Variable Bio.Restriction.Restriction.Sse8387I.results=Bio.Restriction.Restriction.Sse8387I-class.html#results,Variable Bio.Restriction.Restriction.Sse8647I.results=Bio.Restriction.Restriction.Sse8647I-class.html#results,Variable Bio.Restriction.Restriction.Sse9I.results=Bio.Restriction.Restriction.Sse9I-class.html#results,Variable Bio.Restriction.Restriction.SseBI.results=Bio.Restriction.Restriction.SseBI-class.html#results,Variable Bio.Restriction.Restriction.SsiI.results=Bio.Restriction.Restriction.SsiI-class.html#results,Variable Bio.Restriction.Restriction.SspD5I.results=Bio.Restriction.Restriction.SspD5I-class.html#results,Variable Bio.Restriction.Restriction.SspDI.results=Bio.Restriction.Restriction.SspDI-class.html#results,Variable Bio.Restriction.Restriction.SspI.results=Bio.Restriction.Restriction.SspI-class.html#results,Variable Bio.Restriction.Restriction.SstI.results=Bio.Restriction.Restriction.SstI-class.html#results,Variable Bio.Restriction.Restriction.SstII.results=Bio.Restriction.Restriction.SstII-class.html#results,Variable Bio.Restriction.Restriction.Sth132I.results=Bio.Restriction.Restriction.Sth132I-class.html#results,Variable Bio.Restriction.Restriction.Sth302II.results=Bio.Restriction.Restriction.Sth302II-class.html#results,Variable Bio.Restriction.Restriction.StrI.results=Bio.Restriction.Restriction.StrI-class.html#results,Variable Bio.Restriction.Restriction.StsI.results=Bio.Restriction.Restriction.StsI-class.html#results,Variable Bio.Restriction.Restriction.StuI.results=Bio.Restriction.Restriction.StuI-class.html#results,Variable Bio.Restriction.Restriction.StyD4I.results=Bio.Restriction.Restriction.StyD4I-class.html#results,Variable Bio.Restriction.Restriction.StyI.results=Bio.Restriction.Restriction.StyI-class.html#results,Variable Bio.Restriction.Restriction.SwaI.results=Bio.Restriction.Restriction.SwaI-class.html#results,Variable Bio.Restriction.Restriction.TaaI.results=Bio.Restriction.Restriction.TaaI-class.html#results,Variable Bio.Restriction.Restriction.TaiI.results=Bio.Restriction.Restriction.TaiI-class.html#results,Variable Bio.Restriction.Restriction.TaqI.results=Bio.Restriction.Restriction.TaqI-class.html#results,Variable Bio.Restriction.Restriction.TaqII.results=Bio.Restriction.Restriction.TaqII-class.html#results,Variable Bio.Restriction.Restriction.TatI.results=Bio.Restriction.Restriction.TatI-class.html#results,Variable Bio.Restriction.Restriction.TauI.results=Bio.Restriction.Restriction.TauI-class.html#results,Variable Bio.Restriction.Restriction.TfiI.results=Bio.Restriction.Restriction.TfiI-class.html#results,Variable Bio.Restriction.Restriction.TliI.results=Bio.Restriction.Restriction.TliI-class.html#results,Variable Bio.Restriction.Restriction.Tru1I.results=Bio.Restriction.Restriction.Tru1I-class.html#results,Variable Bio.Restriction.Restriction.Tru9I.results=Bio.Restriction.Restriction.Tru9I-class.html#results,Variable Bio.Restriction.Restriction.TscAI.results=Bio.Restriction.Restriction.TscAI-class.html#results,Variable Bio.Restriction.Restriction.TseI.results=Bio.Restriction.Restriction.TseI-class.html#results,Variable Bio.Restriction.Restriction.TsoI.results=Bio.Restriction.Restriction.TsoI-class.html#results,Variable Bio.Restriction.Restriction.Tsp45I.results=Bio.Restriction.Restriction.Tsp45I-class.html#results,Variable Bio.Restriction.Restriction.Tsp4CI.results=Bio.Restriction.Restriction.Tsp4CI-class.html#results,Variable Bio.Restriction.Restriction.Tsp509I.results=Bio.Restriction.Restriction.Tsp509I-class.html#results,Variable Bio.Restriction.Restriction.TspDTI.results=Bio.Restriction.Restriction.TspDTI-class.html#results,Variable Bio.Restriction.Restriction.TspEI.results=Bio.Restriction.Restriction.TspEI-class.html#results,Variable Bio.Restriction.Restriction.TspGWI.results=Bio.Restriction.Restriction.TspGWI-class.html#results,Variable Bio.Restriction.Restriction.TspMI.results=Bio.Restriction.Restriction.TspMI-class.html#results,Variable Bio.Restriction.Restriction.TspRI.results=Bio.Restriction.Restriction.TspRI-class.html#results,Variable Bio.Restriction.Restriction.TssI.results=Bio.Restriction.Restriction.TssI-class.html#results,Variable Bio.Restriction.Restriction.TstI.results=Bio.Restriction.Restriction.TstI-class.html#results,Variable Bio.Restriction.Restriction.TsuI.results=Bio.Restriction.Restriction.TsuI-class.html#results,Variable Bio.Restriction.Restriction.Tth111I.results=Bio.Restriction.Restriction.Tth111I-class.html#results,Variable Bio.Restriction.Restriction.Tth111II.results=Bio.Restriction.Restriction.Tth111II-class.html#results,Variable Bio.Restriction.Restriction.UbaF11I.results=Bio.Restriction.Restriction.UbaF11I-class.html#results,Variable Bio.Restriction.Restriction.UbaF12I.results=Bio.Restriction.Restriction.UbaF12I-class.html#results,Variable Bio.Restriction.Restriction.UbaF13I.results=Bio.Restriction.Restriction.UbaF13I-class.html#results,Variable Bio.Restriction.Restriction.UbaF14I.results=Bio.Restriction.Restriction.UbaF14I-class.html#results,Variable Bio.Restriction.Restriction.UbaF9I.results=Bio.Restriction.Restriction.UbaF9I-class.html#results,Variable Bio.Restriction.Restriction.UbaPI.results=Bio.Restriction.Restriction.UbaPI-class.html#results,Variable Bio.Restriction.Restriction.UnbI.results=Bio.Restriction.Restriction.UnbI-class.html#results,Variable Bio.Restriction.Restriction.Van91I.results=Bio.Restriction.Restriction.Van91I-class.html#results,Variable Bio.Restriction.Restriction.Vha464I.results=Bio.Restriction.Restriction.Vha464I-class.html#results,Variable Bio.Restriction.Restriction.VneI.results=Bio.Restriction.Restriction.VneI-class.html#results,Variable Bio.Restriction.Restriction.VpaK11AI.results=Bio.Restriction.Restriction.VpaK11AI-class.html#results,Variable Bio.Restriction.Restriction.VpaK11BI.results=Bio.Restriction.Restriction.VpaK11BI-class.html#results,Variable Bio.Restriction.Restriction.VspI.results=Bio.Restriction.Restriction.VspI-class.html#results,Variable Bio.Restriction.Restriction.XagI.results=Bio.Restriction.Restriction.XagI-class.html#results,Variable Bio.Restriction.Restriction.XapI.results=Bio.Restriction.Restriction.XapI-class.html#results,Variable Bio.Restriction.Restriction.XbaI.results=Bio.Restriction.Restriction.XbaI-class.html#results,Variable Bio.Restriction.Restriction.XceI.results=Bio.Restriction.Restriction.XceI-class.html#results,Variable Bio.Restriction.Restriction.XcmI.results=Bio.Restriction.Restriction.XcmI-class.html#results,Variable Bio.Restriction.Restriction.XhoI.results=Bio.Restriction.Restriction.XhoI-class.html#results,Variable Bio.Restriction.Restriction.XhoII.results=Bio.Restriction.Restriction.XhoII-class.html#results,Variable Bio.Restriction.Restriction.XmaCI.results=Bio.Restriction.Restriction.XmaCI-class.html#results,Variable Bio.Restriction.Restriction.XmaI.results=Bio.Restriction.Restriction.XmaI-class.html#results,Variable Bio.Restriction.Restriction.XmaIII.results=Bio.Restriction.Restriction.XmaIII-class.html#results,Variable Bio.Restriction.Restriction.XmaJI.results=Bio.Restriction.Restriction.XmaJI-class.html#results,Variable Bio.Restriction.Restriction.XmiI.results=Bio.Restriction.Restriction.XmiI-class.html#results,Variable Bio.Restriction.Restriction.XmnI.results=Bio.Restriction.Restriction.XmnI-class.html#results,Variable Bio.Restriction.Restriction.XspI.results=Bio.Restriction.Restriction.XspI-class.html#results,Variable Bio.Restriction.Restriction.ZraI.results=Bio.Restriction.Restriction.ZraI-class.html#results,Variable Bio.Restriction.Restriction.ZrmI.results=Bio.Restriction.Restriction.ZrmI-class.html#results,Variable Bio.Restriction.Restriction.Zsp2I.results=Bio.Restriction.Restriction.Zsp2I-class.html#results"><a title="Bio.Restriction.Restriction.AanI.results
Bio.Restriction.Restriction.AarI.results
Bio.Restriction.Restriction.AasI.results
Bio.Restriction.Restriction.AatI.results
Bio.Restriction.Restriction.AatII.results
Bio.Restriction.Restriction.AbsI.results
Bio.Restriction.Restriction.Acc16I.results
Bio.Restriction.Restriction.Acc36I.results
Bio.Restriction.Restriction.Acc65I.results
Bio.Restriction.Restriction.AccB1I.results
Bio.Restriction.Restriction.AccB7I.results
Bio.Restriction.Restriction.AccBSI.results
Bio.Restriction.Restriction.AccI.results
Bio.Restriction.Restriction.AccII.results
Bio.Restriction.Restriction.AccIII.results
Bio.Restriction.Restriction.AceIII.results
Bio.Restriction.Restriction.AciI.results
Bio.Restriction.Restriction.AclI.results
Bio.Restriction.Restriction.AclWI.results
Bio.Restriction.Restriction.AcoI.results
Bio.Restriction.Restriction.AcsI.results
Bio.Restriction.Restriction.AcuI.results
Bio.Restriction.Restriction.AcvI.results
Bio.Restriction.Restriction.AcyI.results
Bio.Restriction.Restriction.AdeI.results
Bio.Restriction.Restriction.AfaI.results
Bio.Restriction.Restriction.AfeI.results
Bio.Restriction.Restriction.AfiI.results
Bio.Restriction.Restriction.AflII.results
Bio.Restriction.Restriction.AflIII.results
Bio.Restriction.Restriction.AgeI.results
Bio.Restriction.Restriction.AgsI.results
Bio.Restriction.Restriction.AhaIII.results
Bio.Restriction.Restriction.AhdI.results
Bio.Restriction.Restriction.AhlI.results
Bio.Restriction.Restriction.AjiI.results
Bio.Restriction.Restriction.AjnI.results
Bio.Restriction.Restriction.AjuI.results
Bio.Restriction.Restriction.AleI.results
Bio.Restriction.Restriction.AlfI.results
Bio.Restriction.Restriction.AloI.results
Bio.Restriction.Restriction.AluBI.results
Bio.Restriction.Restriction.AluI.results
Bio.Restriction.Restriction.Alw21I.results
Bio.Restriction.Restriction.Alw26I.results
Bio.Restriction.Restriction.Alw44I.results
Bio.Restriction.Restriction.AlwFI.results
Bio.Restriction.Restriction.AlwI.results
Bio.Restriction.Restriction.AlwNI.results
Bio.Restriction.Restriction.Ama87I.results
Bio.Restriction.Restriction.Aor13HI.results
Bio.Restriction.Restriction.Aor51HI.results
Bio.Restriction.Restriction.ApaBI.results
Bio.Restriction.Restriction.ApaI.results
Bio.Restriction.Restriction.ApaLI.results
Bio.Restriction.Restriction.ApeKI.results
Bio.Restriction.Restriction.ApoI.results
Bio.Restriction.Restriction.ApyPI.results
Bio.Restriction.Restriction.AquII.results
Bio.Restriction.Restriction.AquIII.results
Bio.Restriction.Restriction.AquIV.results
Bio.Restriction.Restriction.ArsI.results
Bio.Restriction.Restriction.AscI.results
Bio.Restriction.Restriction.AseI.results
Bio.Restriction.Restriction.Asi256I.results
Bio.Restriction.Restriction.AsiGI.results
Bio.Restriction.Restriction.AsiSI.results
Bio.Restriction.Restriction.Asp700I.results
Bio.Restriction.Restriction.Asp718I.results
Bio.Restriction.Restriction.AspA2I.results
Bio.Restriction.Restriction.AspCNI.results
Bio.Restriction.Restriction.AspEI.results
Bio.Restriction.Restriction.AspI.results
Bio.Restriction.Restriction.AspLEI.results
Bio.Restriction.Restriction.AspS9I.results
Bio.Restriction.Restriction.AssI.results
Bio.Restriction.Restriction.AsuC2I.results
Bio.Restriction.Restriction.AsuHPI.results
Bio.Restriction.Restriction.AsuI.results
Bio.Restriction.Restriction.AsuII.results
Bio.Restriction.Restriction.AsuNHI.results
Bio.Restriction.Restriction.AvaI.results
Bio.Restriction.Restriction.AvaII.results
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Bio.Restriction.Restriction.RcaI.results
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Bio.Restriction.Restriction.RgaI.results
Bio.Restriction.Restriction.RigI.results
Bio.Restriction.Restriction.RleAI.results
Bio.Restriction.Restriction.RpaB5I.results
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Bio.Restriction.Restriction.RsaNI.results
Bio.Restriction.Restriction.RseI.results
Bio.Restriction.Restriction.Rsr2I.results
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Bio.Restriction.Restriction.SacI.results
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Bio.Restriction.Restriction.SapI.results
Bio.Restriction.Restriction.SaqAI.results
Bio.Restriction.Restriction.SatI.results
Bio.Restriction.Restriction.Sau3AI.results
Bio.Restriction.Restriction.Sau96I.results
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Bio.Restriction.Restriction.SbfI.results
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Bio.Restriction.Restriction.SciI.results
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Bio.Restriction.Restriction.SdaI.results
Bio.Restriction.Restriction.SdeAI.results
Bio.Restriction.Restriction.SdeOSI.results
Bio.Restriction.Restriction.SduI.results
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Bio.Restriction.Restriction.SexAI.results
Bio.Restriction.Restriction.SfaAI.results
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Bio.Restriction.Restriction.SfcI.results
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Bio.Restriction.Restriction.SfoI.results
Bio.Restriction.Restriction.Sfr274I.results
Bio.Restriction.Restriction.Sfr303I.results
Bio.Restriction.Restriction.SfuI.results
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Bio.Restriction.Restriction.SgrAI.results
Bio.Restriction.Restriction.SgrBI.results
Bio.Restriction.Restriction.SgrDI.results
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Bio.Restriction.Restriction.SlaI.results
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Bio.Restriction.Restriction.SmiMI.results
Bio.Restriction.Restriction.SmlI.results
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Bio.Restriction.Restriction.SmuI.results
Bio.Restriction.Restriction.SnaBI.results
Bio.Restriction.Restriction.SnaI.results
Bio.Restriction.Restriction.SpeI.results
Bio.Restriction.Restriction.SphI.results
Bio.Restriction.Restriction.SplI.results
Bio.Restriction.Restriction.SpoDI.results
Bio.Restriction.Restriction.SrfI.results
Bio.Restriction.Restriction.Sse232I.results
Bio.Restriction.Restriction.Sse8387I.results
Bio.Restriction.Restriction.Sse8647I.results
Bio.Restriction.Restriction.Sse9I.results
Bio.Restriction.Restriction.SseBI.results
Bio.Restriction.Restriction.SsiI.results
Bio.Restriction.Restriction.SspD5I.results
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Bio.Restriction.Restriction.SspI.results
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Bio.Restriction.Restriction.Sth132I.results
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Bio.Restriction.Restriction.StyD4I.results
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Bio.Restriction.Restriction.SwaI.results
Bio.Restriction.Restriction.TaaI.results
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Bio.Restriction.Restriction.TaqI.results
Bio.Restriction.Restriction.TaqII.results
Bio.Restriction.Restriction.TatI.results
Bio.Restriction.Restriction.TauI.results
Bio.Restriction.Restriction.TfiI.results
Bio.Restriction.Restriction.TliI.results
Bio.Restriction.Restriction.Tru1I.results
Bio.Restriction.Restriction.Tru9I.results
Bio.Restriction.Restriction.TscAI.results
Bio.Restriction.Restriction.TseI.results
Bio.Restriction.Restriction.TsoI.results
Bio.Restriction.Restriction.Tsp45I.results
Bio.Restriction.Restriction.Tsp4CI.results
Bio.Restriction.Restriction.Tsp509I.results
Bio.Restriction.Restriction.TspDTI.results
Bio.Restriction.Restriction.TspEI.results
Bio.Restriction.Restriction.TspGWI.results
Bio.Restriction.Restriction.TspMI.results
Bio.Restriction.Restriction.TspRI.results
Bio.Restriction.Restriction.TssI.results
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Bio.Restriction.Restriction.TsuI.results
Bio.Restriction.Restriction.Tth111I.results
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Bio.Restriction.Restriction.UbaF11I.results
Bio.Restriction.Restriction.UbaF12I.results
Bio.Restriction.Restriction.UbaF13I.results
Bio.Restriction.Restriction.UbaF14I.results
Bio.Restriction.Restriction.UbaF9I.results
Bio.Restriction.Restriction.UbaPI.results
Bio.Restriction.Restriction.UnbI.results
Bio.Restriction.Restriction.Van91I.results
Bio.Restriction.Restriction.Vha464I.results
Bio.Restriction.Restriction.VneI.results
Bio.Restriction.Restriction.VpaK11AI.results
Bio.Restriction.Restriction.VpaK11BI.results
Bio.Restriction.Restriction.VspI.results
Bio.Restriction.Restriction.XagI.results
Bio.Restriction.Restriction.XapI.results
Bio.Restriction.Restriction.XbaI.results
Bio.Restriction.Restriction.XceI.results
Bio.Restriction.Restriction.XcmI.results
Bio.Restriction.Restriction.XhoI.results
Bio.Restriction.Restriction.XhoII.results
Bio.Restriction.Restriction.XmaCI.results
Bio.Restriction.Restriction.XmaI.results
Bio.Restriction.Restriction.XmaIII.results
Bio.Restriction.Restriction.XmaJI.results
Bio.Restriction.Restriction.XmiI.results
Bio.Restriction.Restriction.XmnI.results
Bio.Restriction.Restriction.XspI.results
Bio.Restriction.Restriction.ZraI.results
Bio.Restriction.Restriction.ZrmI.results
Bio.Restriction.Restriction.Zsp2I.results" class="py-name" href="#" onclick="return doclink('link-3', 'results', 'link-3');">results</a></tt><tt class="py-op">[</tt><tt class="py-string">"version"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">version_res</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt>  <tt class="py-line">        <tt class="py-comment"># Find max lnL</tt> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt>  <tt class="py-line">        <tt class="py-comment"># Example match:</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt>  <tt class="py-line">        <tt class="py-comment"># ln Lmax (unconstrained) = -316.049385</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-string">"ln Lmax"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt>  <tt class="py-line">            <tt id="link-4" class="py-name"><a title="Bio.Restriction.Restriction.AanI.results
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Bio.Restriction.Restriction.BcefI.results
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Bio.Restriction.Restriction.Bme1390I.results
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Bio.Restriction.Restriction.BmgT120I.results
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Bio.Restriction.Restriction.BmtI.results
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Bio.Restriction.Restriction.Bsa29I.results
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Bio.Restriction.Restriction.BsbI.results
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Bio.Restriction.Restriction.BspNCI.results
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Bio.Restriction.Restriction.BsrGI.results
Bio.Restriction.Restriction.BsrI.results
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Bio.Restriction.Restriction.BssAI.results
Bio.Restriction.Restriction.BssECI.results
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Bio.Restriction.Restriction.BssKI.results
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Bio.Restriction.Restriction.Bst2UI.results
Bio.Restriction.Restriction.Bst4CI.results
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Bio.Restriction.Restriction.BstAPI.results
Bio.Restriction.Restriction.BstAUI.results
Bio.Restriction.Restriction.BstBAI.results
Bio.Restriction.Restriction.BstBI.results
Bio.Restriction.Restriction.BstC8I.results
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Bio.Restriction.Restriction.CspCI.results
Bio.Restriction.Restriction.CspI.results
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Bio.Restriction.Restriction.CviAII.results
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Bio.Restriction.Restriction.DdeI.results
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Bio.Restriction.Restriction.MspI.results
Bio.Restriction.Restriction.MspR9I.results
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Bio.Restriction.Restriction.MunI.results
Bio.Restriction.Restriction.Mva1269I.results
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Bio.Restriction.Restriction.Nli3877I.results
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Bio.Restriction.Restriction.NspI.results
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Bio.Restriction.Restriction.OliI.results
Bio.Restriction.Restriction.PabI.results
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Bio.Restriction.Restriction.PaeI.results
Bio.Restriction.Restriction.PaeR7I.results
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Bio.Restriction.Restriction.PauI.results
Bio.Restriction.Restriction.PceI.results
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Bio.Restriction.Restriction.PciSI.results
Bio.Restriction.Restriction.PctI.results
Bio.Restriction.Restriction.PdiI.results
Bio.Restriction.Restriction.PdmI.results
Bio.Restriction.Restriction.PfeI.results
Bio.Restriction.Restriction.Pfl1108I.results
Bio.Restriction.Restriction.Pfl23II.results
Bio.Restriction.Restriction.PflFI.results
Bio.Restriction.Restriction.PflMI.results
Bio.Restriction.Restriction.PfoI.results
Bio.Restriction.Restriction.PhoI.results
Bio.Restriction.Restriction.PinAI.results
Bio.Restriction.Restriction.PlaDI.results
Bio.Restriction.Restriction.Ple19I.results
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Bio.Restriction.Restriction.PshBI.results
Bio.Restriction.Restriction.PsiI.results
Bio.Restriction.Restriction.Psp03I.results
Bio.Restriction.Restriction.Psp124BI.results
Bio.Restriction.Restriction.Psp1406I.results
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Bio.Restriction.Restriction.RseI.results
Bio.Restriction.Restriction.Rsr2I.results
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Bio.Restriction.Restriction.SacI.results
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Bio.Restriction.Restriction.SdeAI.results
Bio.Restriction.Restriction.SdeOSI.results
Bio.Restriction.Restriction.SduI.results
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Bio.Restriction.Restriction.SexAI.results
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Bio.Restriction.Restriction.UbaF13I.results
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Bio.Restriction.Restriction.XmaJI.results
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Bio.Restriction.Restriction.ZrmI.results
Bio.Restriction.Restriction.Zsp2I.results" class="py-name" href="#" onclick="return doclink('link-4', 'results', 'link-3');">results</a></tt><tt class="py-op">[</tt><tt class="py-string">"lnL max"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt>  <tt class="py-line">        <tt class="py-comment"># Find lnL values.</tt> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt>  <tt class="py-line">        <tt class="py-comment"># Example match (lnL = -2021.348300):</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt>  <tt class="py-line">        <tt class="py-comment"># "lnL(ntime: 19  np: 22):  -2021.348300      +0.000000"</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-string">"lnL(ntime:"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt>  <tt class="py-line">            <tt id="link-5" class="py-name"><a title="Bio.Restriction.Restriction.AanI.results
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Bio.Restriction.Restriction.BauI.results
Bio.Restriction.Restriction.BbeI.results
Bio.Restriction.Restriction.Bbr7I.results
Bio.Restriction.Restriction.BbrPI.results
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Bio.Restriction.Restriction.SaqAI.results
Bio.Restriction.Restriction.SatI.results
Bio.Restriction.Restriction.Sau3AI.results
Bio.Restriction.Restriction.Sau96I.results
Bio.Restriction.Restriction.SauI.results
Bio.Restriction.Restriction.SbfI.results
Bio.Restriction.Restriction.ScaI.results
Bio.Restriction.Restriction.SchI.results
Bio.Restriction.Restriction.SciI.results
Bio.Restriction.Restriction.ScrFI.results
Bio.Restriction.Restriction.SdaI.results
Bio.Restriction.Restriction.SdeAI.results
Bio.Restriction.Restriction.SdeOSI.results
Bio.Restriction.Restriction.SduI.results
Bio.Restriction.Restriction.SecI.results
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Bio.Restriction.Restriction.SetI.results
Bio.Restriction.Restriction.SexAI.results
Bio.Restriction.Restriction.SfaAI.results
Bio.Restriction.Restriction.SfaNI.results
Bio.Restriction.Restriction.SfcI.results
Bio.Restriction.Restriction.SfeI.results
Bio.Restriction.Restriction.SfiI.results
Bio.Restriction.Restriction.SfoI.results
Bio.Restriction.Restriction.Sfr274I.results
Bio.Restriction.Restriction.Sfr303I.results
Bio.Restriction.Restriction.SfuI.results
Bio.Restriction.Restriction.SgfI.results
Bio.Restriction.Restriction.SgrAI.results
Bio.Restriction.Restriction.SgrBI.results
Bio.Restriction.Restriction.SgrDI.results
Bio.Restriction.Restriction.SgsI.results
Bio.Restriction.Restriction.SimI.results
Bio.Restriction.Restriction.SinI.results
Bio.Restriction.Restriction.SlaI.results
Bio.Restriction.Restriction.SmaI.results
Bio.Restriction.Restriction.SmiI.results
Bio.Restriction.Restriction.SmiMI.results
Bio.Restriction.Restriction.SmlI.results
Bio.Restriction.Restriction.SmoI.results
Bio.Restriction.Restriction.SmuI.results
Bio.Restriction.Restriction.SnaBI.results
Bio.Restriction.Restriction.SnaI.results
Bio.Restriction.Restriction.SpeI.results
Bio.Restriction.Restriction.SphI.results
Bio.Restriction.Restriction.SplI.results
Bio.Restriction.Restriction.SpoDI.results
Bio.Restriction.Restriction.SrfI.results
Bio.Restriction.Restriction.Sse232I.results
Bio.Restriction.Restriction.Sse8387I.results
Bio.Restriction.Restriction.Sse8647I.results
Bio.Restriction.Restriction.Sse9I.results
Bio.Restriction.Restriction.SseBI.results
Bio.Restriction.Restriction.SsiI.results
Bio.Restriction.Restriction.SspD5I.results
Bio.Restriction.Restriction.SspDI.results
Bio.Restriction.Restriction.SspI.results
Bio.Restriction.Restriction.SstI.results
Bio.Restriction.Restriction.SstII.results
Bio.Restriction.Restriction.Sth132I.results
Bio.Restriction.Restriction.Sth302II.results
Bio.Restriction.Restriction.StrI.results
Bio.Restriction.Restriction.StsI.results
Bio.Restriction.Restriction.StuI.results
Bio.Restriction.Restriction.StyD4I.results
Bio.Restriction.Restriction.StyI.results
Bio.Restriction.Restriction.SwaI.results
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Bio.Restriction.Restriction.TaqI.results
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Bio.Restriction.Restriction.TatI.results
Bio.Restriction.Restriction.TauI.results
Bio.Restriction.Restriction.TfiI.results
Bio.Restriction.Restriction.TliI.results
Bio.Restriction.Restriction.Tru1I.results
Bio.Restriction.Restriction.Tru9I.results
Bio.Restriction.Restriction.TscAI.results
Bio.Restriction.Restriction.TseI.results
Bio.Restriction.Restriction.TsoI.results
Bio.Restriction.Restriction.Tsp45I.results
Bio.Restriction.Restriction.Tsp4CI.results
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Bio.Restriction.Restriction.TspDTI.results
Bio.Restriction.Restriction.TspEI.results
Bio.Restriction.Restriction.TspGWI.results
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Bio.Restriction.Restriction.TspRI.results
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Bio.Restriction.Restriction.TsuI.results
Bio.Restriction.Restriction.Tth111I.results
Bio.Restriction.Restriction.Tth111II.results
Bio.Restriction.Restriction.UbaF11I.results
Bio.Restriction.Restriction.UbaF12I.results
Bio.Restriction.Restriction.UbaF13I.results
Bio.Restriction.Restriction.UbaF14I.results
Bio.Restriction.Restriction.UbaF9I.results
Bio.Restriction.Restriction.UbaPI.results
Bio.Restriction.Restriction.UnbI.results
Bio.Restriction.Restriction.Van91I.results
Bio.Restriction.Restriction.Vha464I.results
Bio.Restriction.Restriction.VneI.results
Bio.Restriction.Restriction.VpaK11AI.results
Bio.Restriction.Restriction.VpaK11BI.results
Bio.Restriction.Restriction.VspI.results
Bio.Restriction.Restriction.XagI.results
Bio.Restriction.Restriction.XapI.results
Bio.Restriction.Restriction.XbaI.results
Bio.Restriction.Restriction.XceI.results
Bio.Restriction.Restriction.XcmI.results
Bio.Restriction.Restriction.XhoI.results
Bio.Restriction.Restriction.XhoII.results
Bio.Restriction.Restriction.XmaCI.results
Bio.Restriction.Restriction.XmaI.results
Bio.Restriction.Restriction.XmaIII.results
Bio.Restriction.Restriction.XmaJI.results
Bio.Restriction.Restriction.XmiI.results
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Bio.Restriction.Restriction.XspI.results
Bio.Restriction.Restriction.ZraI.results
Bio.Restriction.Restriction.ZrmI.results
Bio.Restriction.Restriction.Zsp2I.results" class="py-name" href="#" onclick="return doclink('link-5', 'results', 'link-3');">results</a></tt><tt class="py-op">[</tt><tt class="py-string">"lnL"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt>  <tt class="py-line">            <tt class="py-name">np_res</tt> <tt class="py-op">=</tt> <tt class="py-name">np_re</tt><tt class="py-op">.</tt><tt id="link-6" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-6', 'match', 'link-2');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">np_res</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt>  <tt class="py-line">                <tt class="py-name">num_params</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">np_res</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt>  <tt class="py-line">        <tt class="py-comment"># Find tree lengths.</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt>  <tt class="py-line">        <tt class="py-comment"># Example match: "tree length =   1.71931"</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-string">"tree length"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt>  <tt class="py-line">            <tt id="link-7" class="py-name"><a title="Bio.Restriction.Restriction.AanI.results
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Bio.Restriction.Restriction.AvrII.results
Bio.Restriction.Restriction.AxyI.results
Bio.Restriction.Restriction.BaeGI.results
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Bio.Restriction.Restriction.BamHI.results
Bio.Restriction.Restriction.BanI.results
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Bio.Restriction.Restriction.BarI.results
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Bio.Restriction.Restriction.Bbr7I.results
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Bio.Restriction.Restriction.BbsI.results
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Bio.Restriction.Restriction.Bbv12I.results
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Bio.Restriction.Restriction.BbvI.results
Bio.Restriction.Restriction.BbvII.results
Bio.Restriction.Restriction.BccI.results
Bio.Restriction.Restriction.Bce83I.results
Bio.Restriction.Restriction.BceAI.results
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Bio.Restriction.Restriction.BciVI.results
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Bio.Restriction.Restriction.BfiI.results
Bio.Restriction.Restriction.BfmI.results
Bio.Restriction.Restriction.BfoI.results
Bio.Restriction.Restriction.BfrI.results
Bio.Restriction.Restriction.BfuAI.results
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Bio.Restriction.Restriction.BglI.results
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Bio.Restriction.Restriction.BinI.results
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Bio.Restriction.Restriction.Bme1390I.results
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Bio.Restriction.Restriction.BmeRI.results
Bio.Restriction.Restriction.BmeT110I.results
Bio.Restriction.Restriction.BmgBI.results
Bio.Restriction.Restriction.BmgI.results
Bio.Restriction.Restriction.BmgT120I.results
Bio.Restriction.Restriction.BmiI.results
Bio.Restriction.Restriction.BmrFI.results
Bio.Restriction.Restriction.BmrI.results
Bio.Restriction.Restriction.BmsI.results
Bio.Restriction.Restriction.BmtI.results
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Bio.Restriction.Restriction.Bse3DI.results
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Bio.Restriction.Restriction.BseCI.results
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Bio.Restriction.Restriction.BseSI.results
Bio.Restriction.Restriction.BseX3I.results
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Bio.Restriction.Restriction.BsgI.results
Bio.Restriction.Restriction.Bsh1236I.results
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Bio.Restriction.Restriction.Zsp2I.results" class="py-name" href="#" onclick="return doclink('link-7', 'results', 'link-3');">results</a></tt><tt class="py-op">[</tt><tt class="py-string">"tree length"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt>  <tt class="py-line">        <tt class="py-comment"># Find the estimated tree, only taking the tree if it has</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt>  <tt class="py-line">        <tt class="py-comment"># branch lengths</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-8', 'match', 'link-2');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"\(+"</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-string">":"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt>  <tt class="py-line">                <tt id="link-9" class="py-name"><a title="Bio.Restriction.Restriction.AanI.results
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Bio.Restriction.Restriction.Zsp2I.results" class="py-name" href="#" onclick="return doclink('link-11', 'results', 'link-3');">results</a></tt><tt class="py-op">,</tt> <tt class="py-name">num_params</tt><tt class="py-op">)</tt> </tt>
</div><a name="L49"></a><tt class="py-lineno"> 49</tt>  <tt class="py-line"> </tt>
<a name="parse_parameters"></a><div id="parse_parameters-def"><a name="L50"></a><tt class="py-lineno"> 50</tt> <a class="py-toggle" href="#" id="parse_parameters-toggle" onclick="return toggle('parse_parameters');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.PAML._parse_baseml-module.html#parse_parameters">parse_parameters</a><tt class="py-op">(</tt><tt class="py-param">lines</tt><tt class="py-op">,</tt> <tt class="py-param">results</tt><tt class="py-op">,</tt> <tt class="py-param">num_params</tt><tt class="py-op">)</tt><tt class="py-op">:</tt>  </tt>
</div><a name="L51"></a><tt class="py-lineno"> 51</tt>  <tt class="py-line">    <tt class="py-docstring">"""Parse the various parameters from the file.</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt>  <tt class="py-line">    <tt class="py-name">parameters</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt>  <tt class="py-line">    <tt class="py-name">parameters</tt> <tt class="py-op">=</tt> <tt id="link-12" class="py-name" targets="Function Bio.Phylo.PAML._parse_baseml.parse_parameter_list()=Bio.Phylo.PAML._parse_baseml-module.html#parse_parameter_list"><a title="Bio.Phylo.PAML._parse_baseml.parse_parameter_list" class="py-name" href="#" onclick="return doclink('link-12', 'parse_parameter_list', 'link-12');">parse_parameter_list</a></tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">,</tt> <tt class="py-name">parameters</tt><tt class="py-op">,</tt> <tt class="py-name">num_params</tt><tt class="py-op">)</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt>  <tt class="py-line">    <tt class="py-name">parameters</tt> <tt class="py-op">=</tt> <tt id="link-13" class="py-name" targets="Function Bio.Phylo.PAML._parse_baseml.parse_kappas()=Bio.Phylo.PAML._parse_baseml-module.html#parse_kappas"><a title="Bio.Phylo.PAML._parse_baseml.parse_kappas" class="py-name" href="#" onclick="return doclink('link-13', 'parse_kappas', 'link-13');">parse_kappas</a></tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">,</tt> <tt class="py-name">parameters</tt><tt class="py-op">)</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt>  <tt class="py-line">    <tt class="py-name">parameters</tt> <tt class="py-op">=</tt> <tt id="link-14" class="py-name" targets="Function Bio.Phylo.PAML._parse_baseml.parse_rates()=Bio.Phylo.PAML._parse_baseml-module.html#parse_rates"><a title="Bio.Phylo.PAML._parse_baseml.parse_rates" class="py-name" href="#" onclick="return doclink('link-14', 'parse_rates', 'link-14');">parse_rates</a></tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">,</tt> <tt class="py-name">parameters</tt><tt class="py-op">)</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt>  <tt class="py-line">    <tt class="py-name">parameters</tt> <tt class="py-op">=</tt> <tt id="link-15" class="py-name" targets="Function Bio.Phylo.PAML._parse_baseml.parse_freqs()=Bio.Phylo.PAML._parse_baseml-module.html#parse_freqs"><a title="Bio.Phylo.PAML._parse_baseml.parse_freqs" class="py-name" href="#" onclick="return doclink('link-15', 'parse_freqs', 'link-15');">parse_freqs</a></tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">,</tt> <tt class="py-name">parameters</tt><tt class="py-op">)</tt> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt>  <tt class="py-line">    <tt id="link-16" class="py-name"><a title="Bio.Restriction.Restriction.AanI.results
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Bio.Restriction.Restriction.Zsp2I.results" class="py-name" href="#" onclick="return doclink('link-17', 'results', 'link-3');">results</a></tt> </tt>
</div><a name="L60"></a><tt class="py-lineno"> 60</tt>  <tt class="py-line"> </tt>
<a name="parse_parameter_list"></a><div id="parse_parameter_list-def"><a name="L61"></a><tt class="py-lineno"> 61</tt> <a class="py-toggle" href="#" id="parse_parameter_list-toggle" onclick="return toggle('parse_parameter_list');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.PAML._parse_baseml-module.html#parse_parameter_list">parse_parameter_list</a><tt class="py-op">(</tt><tt class="py-param">lines</tt><tt class="py-op">,</tt> <tt class="py-param">parameters</tt><tt class="py-op">,</tt> <tt class="py-param">num_params</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_parameter_list-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_parameter_list-expanded"><a name="L62"></a><tt class="py-lineno"> 62</tt>  <tt class="py-line">    <tt class="py-docstring">""" Parse the parameters list, which is just an unlabeled list of numeric values.</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">line_num</tt> <tt class="py-keyword">in</tt> <tt id="link-18" class="py-name" targets="Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.range()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#range,Method Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range()=Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Graph.GraphData.range()=Bio.Graphics.GenomeDiagram._Graph.GraphData-class.html#range,Method Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range()=Bio.Graphics.GenomeDiagram._GraphSet.GraphSet-class.html#range,Method Bio.Graphics.GenomeDiagram._Track.Track.range()=Bio.Graphics.GenomeDiagram._Track.Track-class.html#range"><a title="Bio.Graphics.GenomeDiagram._Diagram.Diagram.range
Bio.Graphics.GenomeDiagram._FeatureSet.FeatureSet.range
Bio.Graphics.GenomeDiagram._Graph.GraphData.range
Bio.Graphics.GenomeDiagram._GraphSet.GraphSet.range
Bio.Graphics.GenomeDiagram._Track.Track.range" class="py-name" href="#" onclick="return doclink('link-18', 'range', 'link-18');">range</a></tt><tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">lines</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt>  <tt class="py-line">        <tt class="py-name">line</tt> <tt class="py-op">=</tt> <tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-name">line_num</tt><tt class="py-op">]</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt>  <tt class="py-line">         <tt class="py-comment"># Find all floating point numbers in this line</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt>  <tt class="py-line">        <tt class="py-name">line_floats_res</tt> <tt class="py-op">=</tt> <tt id="link-19" class="py-name"><a title="Bio.Phylo.PAML._parse_baseml.line_floats_re
Bio.Phylo.PAML._parse_codeml.line_floats_re" class="py-name" href="#" onclick="return doclink('link-19', 'line_floats_re', 'link-0');">line_floats_re</a></tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt>  <tt class="py-line">        <tt class="py-name">line_floats</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line_floats_res</tt><tt class="py-op">]</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt>  <tt class="py-line">        <tt class="py-comment"># Get parameter list. This can be useful for specifying starting</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt>  <tt class="py-line">        <tt class="py-comment"># parameters in another run by copying the list of parameters</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt>  <tt class="py-line">        <tt class="py-comment"># to a file called in.baseml. Since the parameters must be in</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt>  <tt class="py-line">        <tt class="py-comment"># a fixed order and format, copying and pasting to the file is</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt>  <tt class="py-line">        <tt class="py-comment"># best. For this reason, they are grabbed here just as a long</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt>  <tt class="py-line">        <tt class="py-comment"># string and not as individual numbers.</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-name">num_params</tt><tt class="py-op">:</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt>  <tt class="py-line">           <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"parameter list"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line</tt><tt class="py-op">.</tt><tt id="link-20" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-20', 'strip', 'link-10');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt>  <tt class="py-line">        <tt class="py-comment"># Find SEs. The same format as parameters above is maintained</tt> </tt>
<a name="L78"></a><tt class="py-lineno"> 78</tt>  <tt class="py-line">        <tt class="py-comment"># since there is a correspondance between the SE format and</tt> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt>  <tt class="py-line">        <tt class="py-comment"># the parameter format.</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt>  <tt class="py-line">        <tt class="py-comment"># Example match:</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt>  <tt class="py-line">        <tt class="py-comment"># "SEs for parameters:</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt>  <tt class="py-line">        <tt class="py-comment"># -1.00000 -1.00000 -1.00000 801727.63247 730462.67590 -1.00000 </tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt>  <tt class="py-line">           <tt class="py-keyword">if</tt> <tt class="py-string">"SEs for parameters:"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-name">line_num</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt>  <tt class="py-line">                <tt class="py-name">SEs_line</tt> <tt class="py-op">=</tt> <tt class="py-name">lines</tt><tt class="py-op">[</tt><tt class="py-name">line_num</tt> <tt class="py-op">+</tt> <tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt>  <tt class="py-line">                <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"SEs"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">SEs_line</tt><tt class="py-op">.</tt><tt id="link-21" class="py-name"><a title="Bio.File.SGMLStripper.strip
Bio.Seq.Seq.strip" class="py-name" href="#" onclick="return doclink('link-21', 'strip', 'link-10');">strip</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt>  <tt class="py-line">           <tt class="py-keyword">break</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">parameters</tt> </tt>
</div><a name="L88"></a><tt class="py-lineno"> 88</tt>  <tt class="py-line"> </tt>
<a name="parse_kappas"></a><div id="parse_kappas-def"><a name="L89"></a><tt class="py-lineno"> 89</tt> <a class="py-toggle" href="#" id="parse_kappas-toggle" onclick="return toggle('parse_kappas');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.PAML._parse_baseml-module.html#parse_kappas">parse_kappas</a><tt class="py-op">(</tt><tt class="py-param">lines</tt><tt class="py-op">,</tt> <tt class="py-param">parameters</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_kappas-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_kappas-expanded"><a name="L90"></a><tt class="py-lineno"> 90</tt>  <tt class="py-line">    <tt class="py-docstring">"""Parse out the kappa parameters.</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt>  <tt class="py-line">    <tt class="py-name">kappa_found</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt>  <tt class="py-line">        <tt class="py-comment"># Find all floating point numbers in this line</tt> </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt>  <tt class="py-line">        <tt class="py-name">line_floats_res</tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.Phylo.PAML._parse_baseml.line_floats_re
Bio.Phylo.PAML._parse_codeml.line_floats_re" class="py-name" href="#" onclick="return doclink('link-22', 'line_floats_re', 'link-0');">line_floats_re</a></tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt>  <tt class="py-line">        <tt class="py-name">line_floats</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line_floats_res</tt><tt class="py-op">]</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt>  <tt class="py-line">        <tt class="py-comment"># Find kappa parameter (F84, HKY85, T92 model)</tt> </tt>
<a name="L98"></a><tt class="py-lineno"> 98</tt>  <tt class="py-line">        <tt class="py-comment"># Example match:</tt> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt>  <tt class="py-line">        <tt class="py-comment"># "Parameters (kappa) in the rate matrix (F84) (Yang 1994 J Mol Evol 39:105-111):</tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt>  <tt class="py-line">        <tt class="py-comment">#    3.00749"</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-string">"Parameters (kappa)"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt>  <tt class="py-line">            <tt class="py-name">kappa_found</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">kappa_found</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt>  <tt class="py-line">            <tt class="py-name">branch_res</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-23', 'match', 'link-2');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"\s(\d+\.\.\d+)"</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">branch_res</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt>  <tt class="py-line">                    <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"kappa"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt>  <tt class="py-line">                <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt>  <tt class="py-line">                    <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"kappa"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt>  <tt class="py-line">                <tt class="py-name">kappa_found</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">parameters</tt><tt class="py-op">.</tt><tt id="link-24" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqIO._index.SeqFileRandomAccess.get()=Bio.SeqIO._index.SeqFileRandomAccess-class.html#get,Method Bio.SeqIO._index.SffRandomAccess.get()=Bio.SeqIO._index.SffRandomAccess-class.html#get,Method Bio.SeqIO._index.SffTrimedRandomAccess.get()=Bio.SeqIO._index.SffTrimedRandomAccess-class.html#get,Method Bio.SeqIO._index.UniprotRandomAccess.get()=Bio.SeqIO._index.UniprotRandomAccess-class.html#get,Method Bio.SeqIO._index._IndexedSeqFileDict.get()=Bio.SeqIO._index._IndexedSeqFileDict-class.html#get,Method Bio.SeqIO._index._SQLiteManySeqFilesDict.get()=Bio.SeqIO._index._SQLiteManySeqFilesDict-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqIO._index.SeqFileRandomAccess.get
Bio.SeqIO._index.SffRandomAccess.get
Bio.SeqIO._index.SffTrimedRandomAccess.get
Bio.SeqIO._index.UniprotRandomAccess.get
Bio.SeqIO._index._IndexedSeqFileDict.get
Bio.SeqIO._index._SQLiteManySeqFilesDict.get" class="py-name" href="#" onclick="return doclink('link-24', 'get', 'link-24');">get</a></tt><tt class="py-op">(</tt><tt class="py-string">"branches"</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt>  <tt class="py-line">                    <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"branches"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt>  <tt class="py-line">                <tt class="py-name">branch</tt> <tt class="py-op">=</tt> <tt class="py-name">branch_res</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt>  <tt class="py-line">                    <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"branches"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">branch</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L117"></a><tt class="py-lineno">117</tt>  <tt class="py-line">                        <tt class="py-op">{</tt><tt class="py-string">"t"</tt><tt class="py-op">:</tt><tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"kappa"</tt><tt class="py-op">:</tt><tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt>  <tt class="py-line">                        <tt class="py-string">"TS"</tt><tt class="py-op">:</tt><tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-string">"TV"</tt><tt class="py-op">:</tt><tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt>  <tt class="py-line">        <tt class="py-comment"># Find kappa under REV</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt>  <tt class="py-line">        <tt class="py-comment"># Example match:</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt>  <tt class="py-line">        <tt class="py-comment"># kappa under REV: 999.00000 145.76453  0.00001  0.00001  0.00001</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-string">"kappa under"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt>  <tt class="py-line">                <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"kappa"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt>  <tt class="py-line">                <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"kappa"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">parameters</tt> </tt>
</div><a name="L128"></a><tt class="py-lineno">128</tt>  <tt class="py-line"> </tt>
<a name="parse_rates"></a><div id="parse_rates-def"><a name="L129"></a><tt class="py-lineno">129</tt> <a class="py-toggle" href="#" id="parse_rates-toggle" onclick="return toggle('parse_rates');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.PAML._parse_baseml-module.html#parse_rates">parse_rates</a><tt class="py-op">(</tt><tt class="py-param">lines</tt><tt class="py-op">,</tt> <tt class="py-param">parameters</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_rates-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_rates-expanded"><a name="L130"></a><tt class="py-lineno">130</tt>  <tt class="py-line">    <tt class="py-docstring">"""Parse the rate parameters.</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt>  <tt class="py-line">    <tt class="py-name">Q_mat_found</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt>  <tt class="py-line">        <tt class="py-comment"># Find all floating point numbers in this line</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt>  <tt class="py-line">        <tt class="py-name">line_floats_res</tt> <tt class="py-op">=</tt> <tt id="link-25" class="py-name"><a title="Bio.Phylo.PAML._parse_baseml.line_floats_re
Bio.Phylo.PAML._parse_codeml.line_floats_re" class="py-name" href="#" onclick="return doclink('link-25', 'line_floats_re', 'link-0');">line_floats_re</a></tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L136"></a><tt class="py-lineno">136</tt>  <tt class="py-line">        <tt class="py-name">line_floats</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line_floats_res</tt><tt class="py-op">]</tt> </tt>
<a name="L137"></a><tt class="py-lineno">137</tt>  <tt class="py-line">        <tt class="py-comment"># Find rate parameters</tt> </tt>
<a name="L138"></a><tt class="py-lineno">138</tt>  <tt class="py-line">        <tt class="py-comment"># Example match: </tt> </tt>
<a name="L139"></a><tt class="py-lineno">139</tt>  <tt class="py-line">        <tt class="py-comment"># "Rate parameters:   999.00000 145.59775  0.00001  0.00001  0.00001"</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-string">"Rate parameters:"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt>  <tt class="py-line">            <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"rate parameters"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt>  <tt class="py-line">        <tt class="py-comment"># Find rates</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt>  <tt class="py-line">        <tt class="py-comment"># Example match: </tt> </tt>
<a name="L144"></a><tt class="py-lineno">144</tt>  <tt class="py-line">        <tt class="py-comment"># "rate:   0.90121  0.96051  0.99831  1.03711  1.10287"</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-string">"rate: "</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt>  <tt class="py-line">            <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"rates"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt>  <tt class="py-line">        <tt class="py-comment"># Find Rate matrix Q &amp; average kappa (REV model)</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt>  <tt class="py-line">        <tt class="py-comment"># Example match:</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt>  <tt class="py-line">        <tt class="py-comment"># Rate matrix Q, Average Ts/Tv =   3.0308</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt>  <tt class="py-line">        <tt class="py-comment">#  -2.483179    1.865730    0.617449    0.000000</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt>  <tt class="py-line">        <tt class="py-comment">#   2.298662   -2.298662    0.000000    0.000000</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt>  <tt class="py-line">        <tt class="py-comment">#   0.335015    0.000000   -0.338059    0.003044</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt>  <tt class="py-line">        <tt class="py-comment">#   0.000000    0.000000    0.004241   -0.004241</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-string">"matrix Q"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt>  <tt class="py-line">            <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"Q matrix"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"matrix"</tt><tt class="py-op">:</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt>  <tt class="py-line">                <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"Q matrix"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"average Ts/Tv"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> \ </tt>
<a name="L158"></a><tt class="py-lineno">158</tt>  <tt class="py-line">                    <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt>  <tt class="py-line">            <tt class="py-name">Q_mat_found</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">Q_mat_found</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt>  <tt class="py-line">            <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"Q matrix"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"matrix"</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-26" class="py-name" targets="Method Bio.Align.MultipleSeqAlignment.append()=Bio.Align.MultipleSeqAlignment-class.html#append,Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append"><a title="Bio.Align.MultipleSeqAlignment.append
Bio.Crystal.Chain.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append" class="py-name" href="#" onclick="return doclink('link-26', 'append', 'link-26');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"Q matrix"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"matrix"</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt>  <tt class="py-line">                <tt class="py-name">Q_mat_found</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt>  <tt class="py-line">        <tt class="py-comment"># Find alpha (gamma shape parameter for variable rates)</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt>  <tt class="py-line">        <tt class="py-comment"># Example match: "alpha (gamma, K=5) = 192.47918"</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-string">"alpha"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt>  <tt class="py-line">            <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"alpha"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">parameters</tt> </tt>
</div><a name="L169"></a><tt class="py-lineno">169</tt>  <tt class="py-line"> </tt>
<a name="parse_freqs"></a><div id="parse_freqs-def"><a name="L170"></a><tt class="py-lineno">170</tt> <a class="py-toggle" href="#" id="parse_freqs-toggle" onclick="return toggle('parse_freqs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Bio.Phylo.PAML._parse_baseml-module.html#parse_freqs">parse_freqs</a><tt class="py-op">(</tt><tt class="py-param">lines</tt><tt class="py-op">,</tt> <tt class="py-param">parameters</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_freqs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_freqs-expanded"><a name="L171"></a><tt class="py-lineno">171</tt>  <tt class="py-line">    <tt class="py-docstring">"""Parse the basepair frequencies.</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt>  <tt class="py-line"><tt class="py-docstring">    """</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt>  <tt class="py-line">    <tt class="py-name">root_re</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">compile</tt><tt class="py-op">(</tt><tt class="py-string">"Note: node (\d+) is root."</tt><tt class="py-op">)</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt>  <tt class="py-line">    <tt class="py-name">branch_freqs_found</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt>  <tt class="py-line">    <tt class="py-keyword">for</tt> <tt class="py-name">line</tt> <tt class="py-keyword">in</tt> <tt class="py-name">lines</tt><tt class="py-op">:</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt>  <tt class="py-line">        <tt class="py-comment"># Find all floating point numbers in this line</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt>  <tt class="py-line">        <tt class="py-name">line_floats_res</tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="Bio.Phylo.PAML._parse_baseml.line_floats_re
Bio.Phylo.PAML._parse_codeml.line_floats_re" class="py-name" href="#" onclick="return doclink('link-27', 'line_floats_re', 'link-0');">line_floats_re</a></tt><tt class="py-op">.</tt><tt class="py-name">findall</tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt>  <tt class="py-line">        <tt class="py-name">line_floats</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">float</tt><tt class="py-op">(</tt><tt class="py-name">val</tt><tt class="py-op">)</tt> <tt class="py-keyword">for</tt> <tt class="py-name">val</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line_floats_res</tt><tt class="py-op">]</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt>  <tt class="py-line">        <tt class="py-comment"># Find base frequencies</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt>  <tt class="py-line">        <tt class="py-comment"># Example match:</tt> </tt>
<a name="L181"></a><tt class="py-lineno">181</tt>  <tt class="py-line">        <tt class="py-comment"># "Base frequencies:   0.20090  0.16306  0.37027  0.26577"  </tt> </tt>
<a name="L182"></a><tt class="py-lineno">182</tt>  <tt class="py-line">        <tt class="py-keyword">if</tt> <tt class="py-string">"Base frequencies"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L183"></a><tt class="py-lineno">183</tt>  <tt class="py-line">            <tt class="py-name">base_frequencies</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L184"></a><tt class="py-lineno">184</tt>  <tt class="py-line">            <tt class="py-name">base_frequencies</tt><tt class="py-op">[</tt><tt class="py-string">"T"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt>  <tt class="py-line">            <tt class="py-name">base_frequencies</tt><tt class="py-op">[</tt><tt class="py-string">"C"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt>  <tt class="py-line">            <tt class="py-name">base_frequencies</tt><tt class="py-op">[</tt><tt class="py-string">"A"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt>  <tt class="py-line">            <tt class="py-name">base_frequencies</tt><tt class="py-op">[</tt><tt class="py-string">"G"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">3</tt><tt class="py-op">]</tt> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt>  <tt class="py-line">            <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"base frequencies"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">base_frequencies</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt>  <tt class="py-line">        <tt class="py-comment"># Find frequencies</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt>  <tt class="py-line">        <tt class="py-comment"># Example match: </tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt>  <tt class="py-line">        <tt class="py-comment"># "freq:   0.90121  0.96051  0.99831  1.03711  1.10287"</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-string">"freq: "</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt>  <tt class="py-line">            <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"rate frequencies"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt>  <tt class="py-line">        <tt class="py-comment"># Find branch-specific frequency parameters</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt>  <tt class="py-line">        <tt class="py-comment"># Example match (note: I think it's possible to have 4 more</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt>  <tt class="py-line">        <tt class="py-comment"># values per line, enclosed in brackets, so I'll account for </tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt>  <tt class="py-line">        <tt class="py-comment"># this):</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt>  <tt class="py-line">        <tt class="py-comment"># (frequency parameters for branches)  [frequencies at nodes] (see Yang &amp; Roberts 1995 fig 1)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt>  <tt class="py-line">        <tt class="py-comment">#</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt>  <tt class="py-line">        <tt class="py-comment"># Node #1  ( 0.25824  0.24176  0.25824  0.24176 )</tt> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt>  <tt class="py-line">        <tt class="py-comment"># Node #2  ( 0.00000  0.50000  0.00000  0.50000 )</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-string">"(frequency parameters for branches)"</tt> <tt class="py-keyword">in</tt> <tt class="py-name">line</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt>  <tt class="py-line">            <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"nodes"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt>  <tt class="py-line">            <tt class="py-name">branch_freqs_found</tt> <tt class="py-op">=</tt> <tt class="py-name">True</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt>  <tt class="py-line">        <tt class="py-keyword">elif</tt> <tt class="py-name">branch_freqs_found</tt> <tt class="py-keyword">is</tt> <tt class="py-name">True</tt><tt class="py-op">:</tt> </tt>
<a name="L206"></a><tt class="py-lineno">206</tt>  <tt class="py-line">            <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt>  <tt class="py-line">                <tt class="py-name">node_res</tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-28" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-28', 'match', 'link-2');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"Node \#(\d+)"</tt><tt class="py-op">,</tt> <tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt>  <tt class="py-line">                <tt class="py-name">node_num</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">node_res</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt>  <tt class="py-line">                <tt id="link-29" class="py-name" targets="Method Bio.Nexus.Trees.Tree.node()=Bio.Nexus.Trees.Tree-class.html#node"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-29', 'node', 'link-29');">node</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"root"</tt><tt class="py-op">:</tt><tt class="py-name">False</tt><tt class="py-op">}</tt> </tt>
<a name="L210"></a><tt class="py-lineno">210</tt>  <tt class="py-line">                <tt id="link-30" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-30', 'node', 'link-29');">node</a></tt><tt class="py-op">[</tt><tt class="py-string">"frequency parameters"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">4</tt><tt class="py-op">]</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">line_floats</tt><tt class="py-op">)</tt> <tt class="py-op">&gt;</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L212"></a><tt class="py-lineno">212</tt>  <tt class="py-line">                    <tt id="link-31" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-31', 'node', 'link-29');">node</a></tt><tt class="py-op">[</tt><tt class="py-string">"base frequencies"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-string">"T"</tt><tt class="py-op">:</tt><tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">4</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt>  <tt class="py-line">                                                <tt class="py-string">"C"</tt><tt class="py-op">:</tt><tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">5</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt>  <tt class="py-line">                                                <tt class="py-string">"A"</tt><tt class="py-op">:</tt><tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">6</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt>  <tt class="py-line">                                                <tt class="py-string">"G"</tt><tt class="py-op">:</tt><tt class="py-name">line_floats</tt><tt class="py-op">[</tt><tt class="py-number">7</tt><tt class="py-op">]</tt><tt class="py-op">}</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt>  <tt class="py-line">                <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"nodes"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">node_num</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name"><a title="Bio.Nexus.Trees.Tree.node" class="py-name" href="#" onclick="return doclink('link-32', 'node', 'link-29');">node</a></tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt>  <tt class="py-line">            <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt>  <tt class="py-line">                <tt class="py-name">root_res</tt> <tt class="py-op">=</tt> <tt class="py-name">root_re</tt><tt class="py-op">.</tt><tt id="link-33" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.triefind.match" class="py-name" href="#" onclick="return doclink('link-33', 'match', 'link-2');">match</a></tt><tt class="py-op">(</tt><tt class="py-name">line</tt><tt class="py-op">)</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt>  <tt class="py-line">                <tt class="py-keyword">if</tt> <tt class="py-name">root_res</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt>  <tt class="py-line">                    <tt class="py-name">root_node</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">root_res</tt><tt class="py-op">.</tt><tt class="py-name">group</tt><tt class="py-op">(</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt>  <tt class="py-line">                    <tt class="py-name">parameters</tt><tt class="py-op">[</tt><tt class="py-string">"nodes"</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-name">root_node</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-string">"root"</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt>\ </tt>
<a name="L222"></a><tt class="py-lineno">222</tt>  <tt class="py-line">                        <tt class="py-name">True</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt>  <tt class="py-line">                    <tt class="py-name">branch_freqs_found</tt> <tt class="py-op">=</tt> <tt class="py-name">False</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt>  <tt class="py-line">    <tt class="py-keyword">return</tt> <tt class="py-name">parameters</tt> </tt>
</div><a name="L225"></a><tt class="py-lineno">225</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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