This is the source code developed for some of the analysis reported in doi:10.1073/pnas.1314702110

The snapshot of the code that was used to run the analyses has itself been assigned a DOI, as follows:

This project depends on https://github.com/rvosa/bio-phylo and https://github.com/bioperl/bioperl-live in addition to the other command line tools specified in the Makefile.

To get a better understanding of how everything is organized, have a look at: http://dx.doi.org/10.1371/journal.pcbi.1000424