Difference between revisions of "PhyloSoC: Interoperable exchange of gene tree reconciliation map:notes"

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* [http://www.nexml.org/ Homepage]
 
* [http://www.nexml.org/ Homepage]
 
* [http://www.w3.org/XML/Schema schema]
 
* [http://www.w3.org/XML/Schema schema]
* Maintainer: [http://rutgervos.blogspot.com/ Rutger Vos] with NESCent
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* Maintainer: [http://rutgervos.blogspot.com/ Rutger Vos] affiliated w/ NESCent (working groups?)
 
* Evolved from NEXUS
 
* Evolved from NEXUS
* Supported by many apps/langauges
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* Software support:
 
** Mesquite
 
** Mesquite
 
** DAMBE
 
** DAMBE
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* [http://www.phyloxml.org/ Homepage]
 
* [http://www.phyloxml.org/ Homepage]
*
 
 
* [http://www.phyloxml.org/documentation/version_1.10/phyloxml_xsd.png schema]
 
* [http://www.phyloxml.org/documentation/version_1.10/phyloxml_xsd.png schema]
* Supported by
+
* [http://groups.yahoo.com/group/phyloxml/ yahoo group]
 +
* Maintainer: [http://www.cmzmasek.net/ Christian Zmasek] affiliated w/ NESCent (working groups?)
 +
* Software support:
 
** [http://www.bioperl.org/wiki/HOWTO:PhyloXML], [http://www.bioperl.org/wiki/Module:Bio::TreeIO::phyloxml BioPerl TreeIO]
 
** [http://www.bioperl.org/wiki/HOWTO:PhyloXML], [http://www.bioperl.org/wiki/Module:Bio::TreeIO::phyloxml BioPerl TreeIO]
** BioRuby, Biopython, jsPhyloSVG, TreeGraph 2, TreeViewJ, TreeGradients, Treevolution, iPhy, Archaeopteryx, phyloxml_converter, decorator, confadd, iTOL, OMA Orthologs Project  
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** BioRuby, Biopython, jsPhyloSVG, TreeGraph 2, TreeViewJ, TreeGradients, Treevolution, iPhy, Archaeopteryx, phyloxml_converter, decorator, confadd, iTOL, OMA Orthologs Project
  
 
== Stuff to be sorted / analyzed ==
 
== Stuff to be sorted / analyzed ==

Revision as of 14:15, 1 June 2011

Description

This is Daniel Packer's PhyloSOC notes page. This page will be used as a scratchpad and information repository during the project.

XML standards

NexML

PhyloXML

  • Homepage
  • schema
  • yahoo group
  • Maintainer: Christian Zmasek affiliated w/ NESCent (working groups?)
  • Software support:
    • [1], BioPerl TreeIO
    • BioRuby, Biopython, jsPhyloSVG, TreeGraph 2, TreeViewJ, TreeGradients, Treevolution, iPhy, Archaeopteryx, phyloxml_converter, decorator, confadd, iTOL, OMA Orthologs Project

Stuff to be sorted / analyzed