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<a href="Bio-module.html">Package Bio</a> ::
Package Phylo
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<h1 class="epydoc">Source Code for <a href="Bio.Phylo-module.html">Package Bio.Phylo</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) 2009 by Eric Talevich (eric.talevich@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-docstring">"""Package for working with phylogenetic trees.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-docstring">See also: http://biopython.org/wiki/Phylo</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt> <tt class="py-line"><tt class="py-name">__docformat__</tt> <tt class="py-op">=</tt> <tt class="py-string">"restructuredtext en"</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt> <tt class="py-line"> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Package Bio=Bio-module.html"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-0', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Package Bio.Phylo=Bio.Phylo-module.html"><a title="Bio.Phylo" class="py-name" href="#" onclick="return doclink('link-1', 'Phylo', 'link-1');">Phylo</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Module Bio.Phylo._io=Bio.Phylo._io-module.html"><a title="Bio.Phylo._io" class="py-name" href="#" onclick="return doclink('link-2', '_io', 'link-2');">_io</a></tt> <tt class="py-keyword">import</tt> <tt id="link-3" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Compass.parse()=Bio.Compass-module.html#parse,Function Bio.Emboss.Primer3.parse()=Bio.Emboss.Primer3-module.html#parse,Method Bio.Entrez.Parser.DataHandler.parse()=Bio.Entrez.Parser.DataHandler-class.html#parse,Function Bio.Entrez.parse()=Bio.Entrez-module.html#parse,Function Bio.ExPASy.Enzyme.parse()=Bio.ExPASy.Enzyme-module.html#parse,Function Bio.ExPASy.Prodoc.parse()=Bio.ExPASy.Prodoc-module.html#parse,Function Bio.ExPASy.Prosite.parse()=Bio.ExPASy.Prosite-module.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Function Bio.Medline.parse()=Bio.Medline-module.html#parse,Function Bio.Motif.parse()=Bio.Motif-module.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.Phylo.NewickIO.Parser.parse()=Bio.Phylo.NewickIO.Parser-class.html#parse,Function Bio.Phylo.NewickIO.parse()=Bio.Phylo.NewickIO-module.html#parse,Function Bio.Phylo.NexusIO.parse()=Bio.Phylo.NexusIO-module.html#parse,Method Bio.Phylo.PhyloXMLIO.Parser.parse()=Bio.Phylo.PhyloXMLIO.Parser-class.html#parse,Function Bio.Phylo.PhyloXMLIO.parse()=Bio.Phylo.PhyloXMLIO-module.html#parse,Function Bio.Phylo._io.parse()=Bio.Phylo._io-module.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.SeqIO.UniprotIO.Parser.parse()=Bio.SeqIO.UniprotIO.Parser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Function Bio.Sequencing.Ace.parse()=Bio.Sequencing.Ace-module.html#parse,Function Bio.Sequencing.Phd.parse()=Bio.Sequencing.Phd-module.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Method Bio.UniGene.UniGene.UniGeneParser.parse()=Bio.UniGene.UniGene.UniGeneParser-class.html#parse,Function Bio.UniGene.parse()=Bio.UniGene-module.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.Compass.RecordParser.parse
Bio.Compass.parse
Bio.Emboss.Primer3.parse
Bio.Entrez.Parser.DataHandler.parse
Bio.Entrez.parse
Bio.ExPASy.Enzyme.parse
Bio.ExPASy.Prodoc.parse
Bio.ExPASy.Prosite.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.Medline.parse
Bio.Motif.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.Phylo.NewickIO.Parser.parse
Bio.Phylo.NewickIO.parse
Bio.Phylo.NexusIO.parse
Bio.Phylo.PhyloXMLIO.Parser.parse
Bio.Phylo.PhyloXMLIO.parse
Bio.Phylo._io.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.parse
Bio.SeqIO.UniprotIO.Parser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.parse
Bio.Sequencing.Phd.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.UniGene.UniGene.UniGeneParser.parse
Bio.UniGene.parse
Bio.Wise.psw.parse" class="py-name" href="#" onclick="return doclink('link-3', 'parse', 'link-3');">parse</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Function Bio.Affy.CelFile.read()=Bio.Affy.CelFile-module.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Blast.NCBIXML.read()=Bio.Blast.NCBIXML-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Function Bio.Compass.read()=Bio.Compass-module.html#read,Function Bio.Emboss.Primer3.read()=Bio.Emboss.Primer3-module.html#read,Function Bio.Emboss.PrimerSearch.read()=Bio.Emboss.PrimerSearch-module.html#read,Method Bio.Entrez.Parser.DataHandler.read()=Bio.Entrez.Parser.DataHandler-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Function Bio.ExPASy.Enzyme.read()=Bio.ExPASy.Enzyme-module.html#read,Function Bio.ExPASy.Prodoc.read()=Bio.ExPASy.Prodoc-module.html#read,Function Bio.ExPASy.Prosite.read()=Bio.ExPASy.Prosite-module.html#read,Function Bio.ExPASy.ScanProsite.read()=Bio.ExPASy.ScanProsite-module.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Function Bio.Medline.read()=Bio.Medline-module.html#read,Function Bio.Motif.Parsers.AlignAce.read()=Bio.Motif.Parsers.AlignAce-module.html#read,Function Bio.Motif.Parsers.MAST.read()=Bio.Motif.Parsers.MAST-module.html#read,Function Bio.Motif.Parsers.MEME.read()=Bio.Motif.Parsers.MEME-module.html#read,Function Bio.Motif.read()=Bio.Motif-module.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Phylo.PAML.baseml.read()=Bio.Phylo.PAML.baseml-module.html#read,Function Bio.Phylo.PAML.codeml.read()=Bio.Phylo.PAML.codeml-module.html#read,Function Bio.Phylo.PAML.yn00.read()=Bio.Phylo.PAML.yn00-module.html#read,Method Bio.Phylo.PhyloXMLIO.Parser.read()=Bio.Phylo.PhyloXMLIO.Parser-class.html#read,Function Bio.Phylo.PhyloXMLIO.read()=Bio.Phylo.PhyloXMLIO-module.html#read,Function Bio.Phylo._io.read()=Bio.Phylo._io-module.html#read,Function Bio.PopGen.GenePop.FileParser.read()=Bio.PopGen.GenePop.FileParser-module.html#read,Function Bio.PopGen.GenePop.LargeFileParser.read()=Bio.PopGen.GenePop.LargeFileParser-module.html#read,Function Bio.PopGen.GenePop.read()=Bio.PopGen.GenePop-module.html#read,Method Bio.SeqIO.SffIO._AddTellHandle.read()=Bio.SeqIO.SffIO._AddTellHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.Sequencing.Ace.read()=Bio.Sequencing.Ace-module.html#read,Function Bio.Sequencing.Phd.read()=Bio.Sequencing.Phd-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read,Function Bio.UniGene.read()=Bio.UniGene-module.html#read"><a title="Bio.Affy.CelFile.read
Bio.AlignIO.read
Bio.Blast.NCBIXML.read
Bio.Cluster.read
Bio.Compass.read
Bio.Emboss.Primer3.read
Bio.Emboss.PrimerSearch.read
Bio.Entrez.Parser.DataHandler.read
Bio.Entrez.read
Bio.ExPASy.Enzyme.read
Bio.ExPASy.Prodoc.read
Bio.ExPASy.Prosite.read
Bio.ExPASy.ScanProsite.read
Bio.File.UndoHandle.read
Bio.Medline.read
Bio.Motif.Parsers.AlignAce.read
Bio.Motif.Parsers.MAST.read
Bio.Motif.Parsers.MEME.read
Bio.Motif.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Phylo.PAML.baseml.read
Bio.Phylo.PAML.codeml.read
Bio.Phylo.PAML.yn00.read
Bio.Phylo.PhyloXMLIO.Parser.read
Bio.Phylo.PhyloXMLIO.read
Bio.Phylo._io.read
Bio.PopGen.GenePop.FileParser.read
Bio.PopGen.GenePop.LargeFileParser.read
Bio.PopGen.GenePop.read
Bio.SeqIO.SffIO._AddTellHandle.read
Bio.SeqIO.read
Bio.Sequencing.Ace.read
Bio.Sequencing.Phd.read
Bio.SwissProt.read
Bio.UniGene.read" class="py-name" href="#" onclick="return doclink('link-4', 'read', 'link-4');">read</a></tt><tt class="py-op">,</tt> <tt id="link-5" class="py-name" targets="Function Bio.AlignIO.write()=Bio.AlignIO-module.html#write,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.write()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#write,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.write()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#write,Method Bio.Phylo.NewickIO.Writer.write()=Bio.Phylo.NewickIO.Writer-class.html#write,Function Bio.Phylo.NewickIO.write()=Bio.Phylo.NewickIO-module.html#write,Function Bio.Phylo.NexusIO.write()=Bio.Phylo.NexusIO-module.html#write,Method Bio.Phylo.PhyloXMLIO.Writer.write()=Bio.Phylo.PhyloXMLIO.Writer-class.html#write,Function Bio.Phylo.PhyloXMLIO.write()=Bio.Phylo.PhyloXMLIO-module.html#write,Function Bio.Phylo._io.write()=Bio.Phylo._io-module.html#write,Function Bio.SeqIO.write()=Bio.SeqIO-module.html#write"><a title="Bio.AlignIO.write
Bio.Graphics.GenomeDiagram._Diagram.Diagram.write
Bio.NeuralNetwork.Gene.Pattern.PatternIO.write
Bio.Phylo.NewickIO.Writer.write
Bio.Phylo.NewickIO.write
Bio.Phylo.NexusIO.write
Bio.Phylo.PhyloXMLIO.Writer.write
Bio.Phylo.PhyloXMLIO.write
Bio.Phylo._io.write
Bio.SeqIO.write" class="py-name" href="#" onclick="return doclink('link-5', 'write', 'link-5');">write</a></tt><tt class="py-op">,</tt> <tt id="link-6" class="py-name" targets="Function Bio.AlignIO.convert()=Bio.AlignIO-module.html#convert,Function Bio.Phylo._io.convert()=Bio.Phylo._io-module.html#convert,Function Bio.SeqIO.convert()=Bio.SeqIO-module.html#convert"><a title="Bio.AlignIO.convert
Bio.Phylo._io.convert
Bio.SeqIO.convert" class="py-name" href="#" onclick="return doclink('link-6', 'convert', 'link-6');">convert</a></tt> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-7" class="py-name"><a title="Bio" class="py-name" href="#" onclick="return doclink('link-7', 'Bio', 'link-0');">Bio</a></tt><tt class="py-op">.</tt><tt id="link-8" class="py-name"><a title="Bio.Phylo" class="py-name" href="#" onclick="return doclink('link-8', 'Phylo', 'link-1');">Phylo</a></tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Module Bio.Phylo._utils=Bio.Phylo._utils-module.html"><a title="Bio.Phylo._utils" class="py-name" href="#" onclick="return doclink('link-9', '_utils', 'link-9');">_utils</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">(</tt><tt id="link-10" class="py-name" targets="Method Bio.Graphics.BasicChromosome.Chromosome.draw()=Bio.Graphics.BasicChromosome.Chromosome-class.html#draw,Method Bio.Graphics.BasicChromosome.ChromosomeSegment.draw()=Bio.Graphics.BasicChromosome.ChromosomeSegment-class.html#draw,Method Bio.Graphics.BasicChromosome.Organism.draw()=Bio.Graphics.BasicChromosome.Organism-class.html#draw,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.draw()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#draw,Method Bio.Graphics.Distribution.BarChartDistribution.draw()=Bio.Graphics.Distribution.BarChartDistribution-class.html#draw,Method Bio.Graphics.Distribution.DistributionPage.draw()=Bio.Graphics.Distribution.DistributionPage-class.html#draw,Method Bio.Graphics.Distribution.LineDistribution.draw()=Bio.Graphics.Distribution.LineDistribution-class.html#draw,Method Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.draw()=Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer-class.html#draw,Method Bio.Graphics.GenomeDiagram._Diagram.Diagram.draw()=Bio.Graphics.GenomeDiagram._Diagram.Diagram-class.html#draw,Method Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.draw()=Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer-class.html#draw,Function Bio.Phylo._utils.draw()=Bio.Phylo._utils-module.html#draw"><a title="Bio.Graphics.BasicChromosome.Chromosome.draw
Bio.Graphics.BasicChromosome.ChromosomeSegment.draw
Bio.Graphics.BasicChromosome.Organism.draw
Bio.Graphics.BasicChromosome._ChromosomeComponent.draw
Bio.Graphics.Distribution.BarChartDistribution.draw
Bio.Graphics.Distribution.DistributionPage.draw
Bio.Graphics.Distribution.LineDistribution.draw
Bio.Graphics.GenomeDiagram._CircularDrawer.CircularDrawer.draw
Bio.Graphics.GenomeDiagram._Diagram.Diagram.draw
Bio.Graphics.GenomeDiagram._LinearDrawer.LinearDrawer.draw
Bio.Phylo._utils.draw" class="py-name" href="#" onclick="return doclink('link-10', 'draw', 'link-10');">draw</a></tt><tt class="py-op">,</tt> <tt id="link-11" class="py-name" targets="Function Bio.Phylo._utils.draw_ascii()=Bio.Phylo._utils-module.html#draw_ascii"><a title="Bio.Phylo._utils.draw_ascii" class="py-name" href="#" onclick="return doclink('link-11', 'draw_ascii', 'link-11');">draw_ascii</a></tt><tt class="py-op">,</tt> <tt id="link-12" class="py-name" targets="Function Bio.Phylo._utils.draw_graphviz()=Bio.Phylo._utils-module.html#draw_graphviz"><a title="Bio.Phylo._utils.draw_graphviz" class="py-name" href="#" onclick="return doclink('link-12', 'draw_graphviz', 'link-12');">draw_graphviz</a></tt><tt class="py-op">,</tt> <tt id="link-13" class="py-name" targets="Function Bio.Phylo._utils.to_networkx()=Bio.Phylo._utils-module.html#to_networkx"><a title="Bio.Phylo._utils.to_networkx" class="py-name" href="#" onclick="return doclink('link-13', 'to_networkx', 'link-13');">to_networkx</a></tt><tt class="py-op">)</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt> <tt class="py-line"> </tt><script type="text/javascript">
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