- 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
- 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)
- 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
- Tree Schema
- Gene Family Tree Schema
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