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).
- LAMARC: Demonstration and Tutorial on Augst 2nd (Peter Beerli)