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

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(Created page with "= 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 =...")
 
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= Description =
 
= Description =
  
This is Daniel Packer's PhyloSOC notes page. This page will be used as a scratchpad and information repository during the project.
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This is Daniel Packer's [http://informatics.nescent.org/wiki/PhyloSoC:_Interoperable_exchange_of_gene_tree_reconciliation_maps PhyloSOC project] notes page. This page will be used as a scratchpad and information repository during the project.
  
 
= XML standards =
 
= XML standards =
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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: Rutger Vos with NESCent
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* Maintainer: [http://rutgervos.blogspot.com/ Rutger Vos], member of NESCent [https://www.nescent.org/wg_evoinfo/Main_Page evoinfo wg]
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* Evolved from NEXUS
 
* Evolved from NEXUS
* Supported by many apps/langauges
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* Software support:
 
** Mesquite
 
** Mesquite
 
** DAMBE
 
** DAMBE
 
** Phylobase/R
 
** Phylobase/R
** BioPerl TreeIO, AlignIO
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** BioPerl TreeIO: http://www.bioperl.org/wiki/Module:Bio::TreeIO::nexml
 
** DendroPy
 
** DendroPy
  
 
== PhyloXML ==
 
== PhyloXML ==
  
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* [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]
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* [http://groups.yahoo.com/group/phyloxml/ yahoo group]
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* [http://www.biomedcentral.com/1471-2105/10/356/ Paper by CM on PhyloXML]
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* Maintainer: [http://www.cmzmasek.net/ Christian Zmasek], member of NESCent [https://www.nescent.org/wg_evoinfo/Main_Page evoinfo wg]
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* Software support:
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** [http://www.bioperl.org/wiki/HOWTO:PhyloXML], [http://www.bioperl.org/wiki/Module:Bio::TreeIO::phyloxml BioPerl TreeIO]
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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 ==
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* [https://pods.iplantcollaborative.org/wiki/display/iptol/Reconciled+Trees+in+XML James Estill's tree rec XML notes]
 
* [https://pods.iplantcollaborative.org/wiki/display/iptol/Reconciled+Trees+in+XML James Estill's tree rec XML notes]
 
* CDAO: http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page
 
* CDAO: http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page
* PhyloWS: https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS#Phyloinformatics_Web_Services_API:_Overview
 
 
* https://pods.iplantcollaborative.org/wiki/display/iptol/Data+Integration
 
* https://pods.iplantcollaborative.org/wiki/display/iptol/Data+Integration
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* https://pods.iplantcollaborative.org/wiki/display/iptol/Name_Resolution_Prototype
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* https://pods.iplantcollaborative.org/wiki/display/iptol/DA_Workshop_Meeting_Notes
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 +
* PhyloWS
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** https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS
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** http://groups.google.com/group/phylows?pli=1
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*** [http://groups.google.com/group/phylows/browse_thread/thread/3ea798b6d4fbff17 In particular, Rutger Vos' Oct 2010 post about event representations]
  
 
[[Category:PhyloSoC]]
 
[[Category:PhyloSoC]]

Latest revision as of 14:24, 1 June 2011

Description

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

XML standards

NexML

PhyloXML

Stuff to be sorted / analyzed