<?xml version="1.0" encoding="ascii"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <title>Bio.Nexus.Nexus</title> <link rel="stylesheet" href="epydoc.css" type="text/css" /> <script type="text/javascript" src="epydoc.js"></script> </head> <body bgcolor="white" text="black" link="blue" vlink="#204080" alink="#204080"> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree link --> <th> <a href="module-tree.html">Trees</a> </th> <!-- Index link --> <th> <a href="identifier-index.html">Indices</a> </th> <!-- Help link --> <th> <a href="help.html">Help</a> </th> <th class="navbar" width="100%"></th> </tr> </table> <table width="100%" cellpadding="0" cellspacing="0"> <tr valign="top"> <td width="100%"> <span class="breadcrumbs"> <a href="Bio-module.html">Package Bio</a> :: <a href="Bio.Nexus-module.html">Package Nexus</a> :: Module Nexus </span> </td> <td> <table cellpadding="0" cellspacing="0"> <!-- hide/show private --> <tr><td align="right"><span class="options">[<a href="javascript:void(0);" class="privatelink" onclick="toggle_private();">hide private</a>]</span></td></tr> <tr><td align="right"><span class="options" >[<a href="frames.html" target="_top">frames</a >] | <a href="Bio.Nexus.Nexus-module.html" target="_top">no frames</a>]</span></td></tr> </table> </td> </tr> </table> <!-- ==================== MODULE DESCRIPTION ==================== --> <h1 class="epydoc">Module Nexus</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html">source code</a></span></p> <p>Nexus class. Parse the contents of a nexus file. Based upon 'NEXUS: An extensible file format for systematic information' Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621</p> <!-- ==================== CLASSES ==================== --> <a name="section-Classes"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Classes</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Classes" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus.NexusError-class.html" class="summary-name">NexusError</a> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus.CharBuffer-class.html" class="summary-name">CharBuffer</a><br /> Helps reading NEXUS-words and characters from a buffer. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus.StepMatrix-class.html" class="summary-name">StepMatrix</a><br /> Calculate a stepmatrix for weighted parsimony. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus.Commandline-class.html" class="summary-name">Commandline</a><br /> Represent a commandline as command and options. </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus.Block-class.html" class="summary-name">Block</a><br /> Represent a NEXUS block with block name and list of commandlines . </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus.Nexus-class.html" class="summary-name">Nexus</a> </td> </tr> </table> <!-- ==================== FUNCTIONS ==================== --> <a name="section-Functions"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Functions</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Functions" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Nexus-module.html#safename" class="summary-sig-name">safename</a>(<span class="summary-sig-arg">name</span>, <span class="summary-sig-arg">mrbayes</span>=<span class="summary-sig-default">False</span>)</span><br /> Return a taxon identifier according to NEXUS standard.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#safename">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="quotestrip"></a><span class="summary-sig-name">quotestrip</span>(<span class="summary-sig-arg">word</span>)</span><br /> Remove quotes and/or double quotes around identifiers.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#quotestrip">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="get_start_end"></a><span class="summary-sig-name">get_start_end</span>(<span class="summary-sig-arg">sequence</span>, <span class="summary-sig-arg">skiplist</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">-</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">?</code><code class="variable-quote">'</code><code class="variable-group">]</code></span>)</span><br /> Return position of first and last character which is not in skiplist (defaults to ['-','?']).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#get_start_end">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_sort_keys_by_values"></a><span class="summary-sig-name">_sort_keys_by_values</span>(<span class="summary-sig-arg">p</span>)</span><br /> Returns a sorted list of keys of p sorted by values of p.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_sort_keys_by_values">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_make_unique"></a><span class="summary-sig-name">_make_unique</span>(<span class="summary-sig-arg">l</span>)</span><br /> Check that all values in list are unique and return a pruned and sorted list.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_make_unique">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_unique_label"></a><span class="summary-sig-name">_unique_label</span>(<span class="summary-sig-arg">previous_labels</span>, <span class="summary-sig-arg">label</span>)</span><br /> Returns a unique name if label is already in previous_labels.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_unique_label">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_seqmatrix2strmatrix"></a><span class="summary-sig-name">_seqmatrix2strmatrix</span>(<span class="summary-sig-arg">matrix</span>)</span><br /> Converts a Seq-object matrix to a plain sequence-string matrix.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_seqmatrix2strmatrix">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_compact4nexus"></a><span class="summary-sig-name">_compact4nexus</span>(<span class="summary-sig-arg">orig_list</span>)</span><br /> Transform [1 2 3 5 6 7 8 12 15 18 20] (baseindex 0, used in the Nexus class) into '2-4 6-9 13-19\3 21' (baseindex 1, used in programs like Paup or MrBayes.).</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_compact4nexus">source code</a></span> </td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Nexus-module.html#combine" class="summary-sig-name">combine</a>(<span class="summary-sig-arg">matrices</span>)</span><br /> Combine matrices in [(name,nexus-instance),...] and return new nexus instance.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#combine">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Nexus-module.html#_kill_comments_and_break_lines" class="summary-sig-name" onclick="show_private();">_kill_comments_and_break_lines</a>(<span class="summary-sig-arg">text</span>)</span><br /> Delete []-delimited comments out of a file and break into lines separated by ';'.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_kill_comments_and_break_lines">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a href="Bio.Nexus.Nexus-module.html#_adjust_lines" class="summary-sig-name" onclick="show_private();">_adjust_lines</a>(<span class="summary-sig-arg">lines</span>)</span><br /> Adjust linebreaks to match ';', strip leading/trailing whitespace</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_adjust_lines">source code</a></span> </td> </tr> </table> </td> </tr> <tr class="private"> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr> <td><span class="summary-sig"><a name="_replace_parenthesized_ambigs"></a><span class="summary-sig-name">_replace_parenthesized_ambigs</span>(<span class="summary-sig-arg">seq</span>, <span class="summary-sig-arg">rev_ambig_values</span>)</span><br /> Replaces ambigs in xxx(ACG)xxx format by IUPAC ambiguity code.</td> <td align="right" valign="top"> <span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_replace_parenthesized_ambigs">source code</a></span> </td> </tr> </table> </td> </tr> </table> <!-- ==================== VARIABLES ==================== --> <a name="section-Variables"></a> <table class="summary" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Variables</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-Variables" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="C"></a><span class="summary-name">C</span> = <code title="False">False</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="INTERLEAVE"></a><span class="summary-name">INTERLEAVE</span> = <code title="70">70</code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus-module.html#SPECIAL_COMMANDS" class="summary-name">SPECIAL_COMMANDS</a> = <code title="['charstatelabels', 'charlabels', 'taxlabels', 'taxset', 'charset', 'charpartition', 'taxpartition', 'matrix', ..."><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">charstatelabels</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">charlabels</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">taxlabel</code><code class="variable-ellipsis">...</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus-module.html#KNOWN_NEXUS_BLOCKS" class="summary-name">KNOWN_NEXUS_BLOCKS</a> = <code title="['trees', 'data', 'characters', 'taxa', 'sets', 'codons']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">trees</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">data</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">characters</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">taxa</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-ellipsis">...</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="PUNCTUATION"></a><span class="summary-name">PUNCTUATION</span> = <code title="'()[]{}/\\,;:=*\'"`+-<>'"><code class="variable-quote">'</code><code class="variable-string">()[]{}/\\,;:=*\'"`+-<></code><code class="variable-quote">'</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus-module.html#MRBAYESSAFE" class="summary-name">MRBAYESSAFE</a> = <code title="'abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890_'"><code class="variable-quote">'</code><code class="variable-string">abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTU</code><code class="variable-ellipsis">...</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="WHITESPACE"></a><span class="summary-name">WHITESPACE</span> = <code title="''' \t '''"><code class="variable-quote">'</code><code class="variable-string"> \t\n</code><code class="variable-quote">'</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="SPECIALCOMMENTS"></a><span class="summary-name">SPECIALCOMMENTS</span> = <code title="['&']"><code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">&</code><code class="variable-quote">'</code><code class="variable-group">]</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="CHARSET"></a><span class="summary-name">CHARSET</span> = <code title="'chars'"><code class="variable-quote">'</code><code class="variable-string">chars</code><code class="variable-quote">'</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="TAXSET"></a><span class="summary-name">TAXSET</span> = <code title="'taxa'"><code class="variable-quote">'</code><code class="variable-string">taxa</code><code class="variable-quote">'</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a name="CODONPOSITIONS"></a><span class="summary-name">CODONPOSITIONS</span> = <code title="'codonpositions'"><code class="variable-quote">'</code><code class="variable-string">codonpositions</code><code class="variable-quote">'</code></code> </td> </tr> <tr> <td width="15%" align="right" valign="top" class="summary"> <span class="summary-type"> </span> </td><td class="summary"> <a href="Bio.Nexus.Nexus-module.html#DEFAULTNEXUS" class="summary-name">DEFAULTNEXUS</a> = <code title="'''#NEXUS begin data; dimensions ntax=0 nchar=0; format datatype=dna; end; '''"><code class="variable-quote">'</code><code class="variable-string">#NEXUS\nbegin data; dimensions ntax=0 nchar=0;</code><code class="variable-ellipsis">...</code></code> </td> </tr> </table> <!-- ==================== FUNCTION DETAILS ==================== --> <a name="section-FunctionDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Function Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-FunctionDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="safename"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">safename</span>(<span class="sig-arg">name</span>, <span class="sig-arg">mrbayes</span>=<span class="sig-default">False</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#safename">source code</a></span> </td> </tr></table> <p>Return a taxon identifier according to NEXUS standard. Wrap quotes around names with punctuation or whitespace, and double single quotes. mrbayes=True: write names without quotes, whitespace or punctuation for mrbayes.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="combine"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">combine</span>(<span class="sig-arg">matrices</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#combine">source code</a></span> </td> </tr></table> <p>Combine matrices in [(name,nexus-instance),...] and return new nexus instance.</p> <p>combined_matrix=combine([(name1,nexus_instance1),(name2,nexus_instance2),...] Character sets, character partitions and taxon sets are prefixed, readjusted and present in the combined matrix.</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_kill_comments_and_break_lines"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_kill_comments_and_break_lines</span>(<span class="sig-arg">text</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_kill_comments_and_break_lines">source code</a></span> </td> </tr></table> <p>Delete []-delimited comments out of a file and break into lines separated by ';'.</p> <p>stripped_text=_kill_comments_and_break_lines(text): Nested and multiline comments are allowed. [ and ] symbols within single or double quotes are ignored, newline ends a quote, all symbols with quotes are treated the same (thus not quoting inside comments like [this character ']' ends a comment]) Special [&...] and [\...] comments remain untouched, if not inside standard comment. Quotes inside special [& and [\ are treated as normal characters, but no nesting inside these special comments allowed (like [& [\ ]]). ';' ist deleted from end of line.</p> <p>NOTE: this function is very slow for large files, and obsolete when using C extension cnexus</p> <dl class="fields"> </dl> </td></tr></table> </div> <a name="_adjust_lines"></a> <div class="private"> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <table width="100%" cellpadding="0" cellspacing="0" border="0"> <tr valign="top"><td> <h3 class="epydoc"><span class="sig"><span class="sig-name">_adjust_lines</span>(<span class="sig-arg">lines</span>)</span> </h3> </td><td align="right" valign="top" ><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#_adjust_lines">source code</a></span> </td> </tr></table> <p>Adjust linebreaks to match ';', strip leading/trailing whitespace</p> <p>list_of_commandlines=_adjust_lines(input_text) Lines are adjusted so that no linebreaks occur within a commandline (except matrix command line)</p> <dl class="fields"> </dl> </td></tr></table> </div> <br /> <!-- ==================== VARIABLES DETAILS ==================== --> <a name="section-VariablesDetails"></a> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr bgcolor="#70b0f0" class="table-header"> <td colspan="2" class="table-header"> <table border="0" cellpadding="0" cellspacing="0" width="100%"> <tr valign="top"> <td align="left"><span class="table-header">Variables Details</span></td> <td align="right" valign="top" ><span class="options">[<a href="#section-VariablesDetails" class="privatelink" onclick="toggle_private();" >hide private</a>]</span></td> </tr> </table> </td> </tr> </table> <a name="SPECIAL_COMMANDS"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">SPECIAL_COMMANDS</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">charstatelabels</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">charlabels</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">taxlabels</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">taxset</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">charset</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">charpartition</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">taxpartition</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-quote">'</code><code class="variable-string">matrix</code><code class="variable-quote">'</code><code class="variable-op">,</code> <code class="variable-ellipsis">...</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="KNOWN_NEXUS_BLOCKS"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">KNOWN_NEXUS_BLOCKS</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-group">[</code><code class="variable-quote">'</code><code class="variable-string">trees</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">data</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">characters</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">taxa</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">sets</code><code class="variable-quote">'</code><code class="variable-op">, </code><code class="variable-quote">'</code><code class="variable-string">codons</code><code class="variable-quote">'</code><code class="variable-group">]</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="MRBAYESSAFE"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">MRBAYESSAFE</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-quote">'</code><code class="variable-string">abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890_</code><code class="variable-quote">'</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <a name="DEFAULTNEXUS"></a> <div> <table class="details" border="1" cellpadding="3" cellspacing="0" width="100%" bgcolor="white"> <tr><td> <h3 class="epydoc">DEFAULTNEXUS</h3> <dl class="fields"> </dl> <dl class="fields"> <dt>Value:</dt> <dd><table><tr><td><pre class="variable"> <code class="variable-quote">'''</code><code class="variable-string">#NEXUS</code> <code class="variable-string">begin data; dimensions ntax=0 nchar=0; format datatype=dna; end; </code><code class="variable-quote">'''</code> </pre></td></tr></table> </dd> </dl> </td></tr></table> </div> <br /> <!-- ==================== NAVIGATION BAR ==================== --> <table class="navbar" border="0" width="100%" cellpadding="0" bgcolor="#a0c0ff" cellspacing="0"> <tr valign="middle"> <!-- Tree 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