PGAP

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Introduction

Usage

Step 3 Running PGAP

For PAGP, there are five functional modules:

  • functional genes into clusters
  • ascertain pan-genome profile
  • genetic variation of functional genes
  • species evolution analysis
  • function enrichment of gene clusters

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
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