Difference between revisions of "PhyloSoC:Biopython support for parsing and writing phyloXML"

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[[User:EricTalevich|Eric Talevich]], University of Georgia
 
[[User:EricTalevich|Eric Talevich]], University of Georgia
  
Mentored by [http://bcbio.wordpress.com/ Brad Chapman] and [http://monochrome-effect.net/ Christian Zmasek]
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Mentored by [http://bcbio.wordpress.com/ Brad Chapman] and [http://www.cmzmasek.net/ Christian Zmasek]
  
 
==Abstract==
 
==Abstract==
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==See also==
 
==See also==
  
* [http://github.com/etal/biopython/tree/phyloxml/Bio/PhyloXML Project plan]
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* [http://spreadsheets.google.com/pub?key=puFMq1smOMEo20j0h5Dg9fA&single=true&gid=0&output=html Project plan]
  
* [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798969 GSoC project page]
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* [http://biopython.org/wiki/PhyloXML Biopython wiki documentation]
  
* [http://biopython.org/wiki/Active_projects Biopython wiki]
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* [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798969 GSoC project proposal]
  
* [http://github.com/etal/biopython/tree/phyloxml GitHub branch]
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* [http://github.com/etal/biopython/tree/phyloxml GitHub branch] (source code)
  
 
===Related projects===
 
===Related projects===
  
* [http://www.bioperl.org/wiki/Phyloxml_Project_Demo BioPerl implementation (2008)]
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* [http://www.bioperl.org/wiki/Phyloxml_Project_Demo BioPerl implementation] (2008)
  
* [[PhyloSoC:PhyloXML_support_in_BioRuby|BioRuby implementation (current)]]
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* [[PhyloSoC:PhyloXML_support_in_BioRuby|BioRuby implementation]] (current)
  
 
[[Category:Phyloxml]]
 
[[Category:Phyloxml]]
 
[[Category: PhyloSoC]]
 
[[Category: PhyloSoC]]

Latest revision as of 16:22, 23 December 2010

Author

Eric Talevich, University of Georgia

Mentored by Brad Chapman and Christian Zmasek

Abstract

PhyloXML is an XML format for phylogenetic trees, designed to allow storing information about the trees themselves (such as branch lengths and multiple support values) along with data such as taxonomic and genomic annotations. Connecting these pieces of evolutionary information in a standard format is key for comparative genomics.

A Bioperl driver for phyloXML was created during the 2008 Summer of Code; this project aims to build a similar module for the popular Biopython package.

See also

Related projects