Introduction

Usage

For PAGP, there are five functional modules:

functional genes into clusters (invoked on commandline via --cluster)
ascertain pan-genome profile (invoked on commandline via --pangenome)
genetic variation of functional genes (invoked on commandline via --variation)
species evolution analysis (invoked on commandline via --evolution)
function enrichment of gene clusters (invoked on commandline via --function)

Example command for this stage:

The following commands trigger all these analysis modules with the default parameters.

PGAP.pl -strains nickname1+...+nicknameN -input <input_dir> -output <out_dir> --cluster --pangenome --variation --evolution --function -method MP|GF