BAli-Phy 2.2.0 is finally released after more than two years of
This release does not have too many new features, because much of
the core infrastructure was rewritten.
The main new features are: (http://www.bali-phy.org/news.php#2.2.0
- site-dependent codon models: M1a, M2a, M2a_Test
- branch-site codon models: branch-site[2,HKY,F3x4]
- inference of ancestral sequences at internal nodes
You can download binaries for Linux, Mac, and Windows here:
You can read the updated manual here:
If you have any trouble using bali-phy, please post your
to firstname.lastname@example.org and I will try
to respond quickly.