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 <><