Phylogenetic_Aware_Parsing_Script
‘Phylogenetic Aware Parsing Script’ (PAPS for short) is the last of a pipeline of three Perl scripts which allows the user to produce lists of homologous genes (proteins clustered using MCL) based on their taxonomic occupancy; this allows the user to infer the patterns of gene gains and losses across a phylogeny which can be customized by the user.
