living1069/phylosub

Deprecation notice

PhyloSub has been replaced by PhyloWGS, which performs the same function as PhyloSub but with numerous improvements. Prime amongst these is the ability to integrate copy number variation (CNV) data. But we also have added parsing support for a number of mutation callers and subclonal CNV callers. PhyloWGS can, however, run without any CNV information -- simply run with an empty cnv_data.txt, and PhyloWGS will function like PhyloSub and will produce phylogenies based solely on single-nucleotide somatic mutation (SSM) frequency.

This Python/C++ code is the accompanying software for the paper:

Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein and Quaid Morris, Inferring clonal evolution of tumors from single nucleotide somatic mutations, BMC Bioinformatics 15:35, 2014.

Please check the README file in c++ folder for instructions to run the software.