TR_Tools and Software

Visualization

• ARCHAEOPTERYX, Visualization of annotated phylogenetic trees
  • Can be integrated as a java applet
  • Accepts PhyloXML, Newick, NHX as input
• PRIMETV, visualization of reconciled trees
  • Draws reconciled trees
  • CLI interface – can be integrated in web app

Host/Parasite Reconciliation

• PARAFIT, a program that tests host-parasite evolution and AXPARAFIT, faster version of PARAFIT
• COPYCAT, an easy and fast access to cophylogenetic analyses (wrapper for PARAFIT)

Gene/Species Reconciliation

• NOTUNG, gene tree reconstruction or post hoc analysis of any rooted tree (with bootstrap values) for alternative hypothesis evaluation
• SOFTPARSMAP, uses ’soft parsimony’ to root gene trees by mapping them on to a species tree

Database Schema

• Tree Schema
  • Crimson - http://www.phylo.org/sub_sections/crimson/
  • TreeBase II - http://www.phylo.org/sub_sections/databases
  • BioSQL-PhyloDB - http://www.biosql.org/wiki/Extensions, http://www.biosql.org/wiki/PhyloDBSchema
  • Chado-PhylogenyModule - http://gmod.org/wiki/Chado_Phylogeny_Module
• Gene Family Tree Schema
  • EnsembleCompara - http://pre.ensembl.org/info/docs/api/compara/compara_schema.html
  • TreeFam - http://www.treefam.org/#introduction

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