m3l

M3L extends PhyML version 3.0 with the following features: A multiple branch length mixture model (see Kolaczkowski and Thornton, MBE 2008) Simultaneous optimization of all free parameters, including branch lengths, using BFGS. Empirical Bayes estimation of posterior probabilities of clades (see Kolaczkowski and Thornton, MBE 2007) INSTALLATION For Mac users, follow the link for "Downloads" near the top of this page. You will find a precompiled binary that works on most Intel-based Macs with OSX 10.7 and later. To run the program, open your terminal, navigate to the folder containing the downloaded file, and then run the file as "phyml+m3l". For source code, follow the link for "Source" above, and then follow the link to "Download zip." Inside the zip file, you will find source code (written in C). You will also find installation instructions in a text f