View source for PhyloSoC: Interoperable exchange of gene tree reconciliation map:notes

= Description =

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 =

== NexML ==

* [http://www.nexml.org/ Homepage]
* [http://www.w3.org/XML/Schema schema]
* Maintainer: [http://rutgervos.blogspot.com/ Rutger Vos], member of NESCent [https://www.nescent.org/wg_evoinfo/Main_Page evoinfo wg]

* Evolved from NEXUS
* Software support:
** Mesquite
** DAMBE
** Phylobase/R
** BioPerl TreeIO: http://www.bioperl.org/wiki/Module:Bio::TreeIO::nexml
** DendroPy

== PhyloXML ==

* [http://www.phyloxml.org/ Homepage]
* [http://www.phyloxml.org/documentation/version_1.10/phyloxml_xsd.png schema]
* [http://groups.yahoo.com/group/phyloxml/ yahoo group]
* [http://www.biomedcentral.com/1471-2105/10/356/ Paper by CM on PhyloXML]
* Maintainer: [http://www.cmzmasek.net/ Christian Zmasek], member of NESCent [https://www.nescent.org/wg_evoinfo/Main_Page evoinfo wg]
* Software support:
** [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

== Stuff to be sorted / analyzed ==

* [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
* https://pods.iplantcollaborative.org/wiki/display/iptol/Data+Integration
* https://pods.iplantcollaborative.org/wiki/display/iptol/Name_Resolution_Prototype
* https://pods.iplantcollaborative.org/wiki/display/iptol/DA_Workshop_Meeting_Notes

* PhyloWS
** https://www.nescent.org/wg/evoinfo/index.php?title=PhyloWS
** http://groups.google.com/group/phylows?pli=1
*** [http://groups.google.com/group/phylows/browse_thread/thread/3ea798b6d4fbff17 In particular, Rutger Vos' Oct 2010 post about event representations]

[[Category:PhyloSoC]]