BAli-Phy 2.3 is released

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Benjamin Redelings

Jun 8, 2014, 4:26:45 PM6/8/14
BAli-Phy version 2.3 is now freely available for download. BAli-Phy is a Bayesian MCMC program for estimating phylogenies and sequence alignments jointly from unaligned sequence data.  Version 2.3 should be faster than version 2.2 and generates prettier HTML reports.

The main new features in version 2.3 are: (
- Speed increases relative to 2.2
- - Generate prettier HTML reports.
- Fix and enable M1a, M2a, M2a_Test, M7, M8, M8a, M8a_Test.
- Handle ambiguous nucleotides K, B, D, M, H, and V in nucleotide and codon alphabets.
The model framework and alignment MCMC were both rewritten as well.

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 questions to  I should be able to respond fairly quickly.

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