PhyloSoC: Interoperable exchange of gene tree reconciliation map:notes

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

• Homepage
• schema
• Maintainer: Rutger Vos, member of NESCent evoinfo wg

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

PhyloXML

• Homepage
• schema
• yahoo group
• Paper by CM on PhyloXML
• Maintainer: Christian Zmasek, member of NESCent evoinfo wg
• 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

• 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
    • In particular, Rutger Vos' Oct 2010 post about event representations