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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).