This code was written to process data in our Metazoan phylogeny paper. Please consider citing it if you are using the scripts:

ML Borowiec, EK Lee, JC Chiu, DC Plachetzki (2015) Extracting phylogenetic signal and accounting for bias in whole-genome data sets supports the Ctenophora as sister to remaining Metazoa. BMC genomics 16 (1), 987.