PhyloSoC: Interoperable exchange of gene tree reconciliation map:notes
From Phyloinformatics
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