Phylogenetic tree building and analysis
- BEAST2 - software package includes BEAST, BEAUti, LogCombiner, TreeAnnotator
- RAxML (and many other programs)
- Comprehensive list of Phylogeny programs
Post-Hoc Tree Analysis or manipulation
- DendroPy (Fantastic for summarizing posteriors, distance calculations, and simulation)
- Newick Utilities (Rerooting and tree parsing from the command line)
Tree Viewing and Plotting
- 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 8 2019 (Peter Beerli)
- Migrate main website: Download, Manual, Blog/Tutorials, Information on speed, citation of MIGRATE in the literature.
- Migrate tutorial 2018
- Migrate tutorial 2017, 2015 Migrate tutorial: Tutorial for the course 2014 (an older version can be found here tutorial on the Migrate tutorial website)
- Migrate support Google Group