This directory contains bioinformatics software, some of which was written
as a member of the Berkeley Phylogenomics Group
http://phylogenomics.berkeley.edu
and some of which was written as a member of the Center for Evolution and
Cancer
http://cancer.ucsf.edu/evolution

compute_alignment_conservation.c - Program to compute the conservation of a
multiple-sequence alignment in a2m format.
PHOG - The Berkeley PHOG software for computing orthologs. Incorporates branch
length information, supporting coarser or more refined clustering based on
evolutionary distance.
bw9 - Model of tumor progression including driver, housekeeper, passenger, and
mutator mutations (when enough mutator mutations accumulate, the mutation rate
becomes elevated).