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A perl based pipeline for clustering genes and ascertaining pan-genomes of prokaryotes.

Usage is the principle executable. Typing it without any arguments will give a helpful output.

Step 3 Running PGAP

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


  • The main options have single dash options: 1) -strains 2) -input 3) -output 4) -method
  • The five modules can be run separately or collectively
  • a --thread for setting the number of option is avilable