Phylogenetic tree building and analysis
- BEAST - software package includes BEAST, BEAUti, LogCombiner, TreeAnnotator
- RAxML (and many other programs)
- Comprehensive list of Phylogeny programs
- Bugs in a Box: A Macintosh program and its (python) source code to show the coalescence process (but still does not draw a tree).
- MCMC example software from John Huelsenbeck
- LAMARC: (If you want to know more about Lamarc talk to Peter Beerli)
- MIGRATE: Demonstration and Tutorial on August 4 (Peter Beerli)