‘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.
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Input
Output
Create_DBs.pl
Phylogenetic Aware Parsing Script.pl
README.docx
Tree.txt