Announcing BAli-Phy 2.0.0

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Benjamin Redelings

Aug 31, 2007, 3:07:25 PM8/31/07
BAli-Phy is a computer program for co-estimating alignments and
phylogenies in a Bayesian statistical framework. It avoids bias
towards a guide tree by merging alignment estimation and phylogeny
into a single step and summing over all alignments weighted by their
posterior probability. BAli-Phy understands DNA, RNA, protein, and
codon data, and can account for rate heterogeneity among sites using
either a log-normal or gamma distribution.

We have recently released version BAli-Phy 2.0.0 with many
improvements. It is
available on Linux, Windows, and Mac, and the source code is freely
available. Improvements include:
* Ease of use - and the User's Guide is much improved.
* Use Tracer for visualizing MCMC output and results.
* Additional plots to visualize alignment uncertainty.
* Implement the GTR model for nucletides.
* Handle R,Y,W,S nucleotide patterns in DNA/RNA and codon alphabets.
* Easier (optional) compilation [autoconf]
* Improved SPR proposals for jointly proposing tree & alignment.

A larger, but still incomplete, list of improvements is here:

To download the software:

To view the User's Guide:

Benjamin Redelings I <><

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