/
TR_Tools and Software

TR_Tools and Software

By Sheldon McKay
Apr 27, 2010

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