Difference between revisions of "PGAP"
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For PAGP, there are five functional modules: | For PAGP, there are five functional modules: | ||
| − | * functional genes into clusters | + | * functional genes into clusters (invoked on commandline via '''--cluster''') |
| − | * ascertain pan-genome profile | + | * ascertain pan-genome profile (invoked on commandline via '''--pangenome''') |
| − | * genetic variation of functional genes | + | * genetic variation of functional genes (invoked on commandline via '''--variation''') |
| − | * species evolution analysis | + | * species evolution analysis (invoked on commandline via '''--evolution''') |
| − | * function enrichment of gene clusters | + | * function enrichment of gene clusters (invoked on commandline via '''--function''') |
Example command for this stage: | Example command for this stage: | ||
The following commands trigger all these analysis modules with the default parameters. | 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 | + | PGAP.pl -strains nickname1+...+nicknameN -input <input_dir> -output <out_dir> --cluster --pangenome --variation --evolution --function -method MP|GF |
Revision as of 16:00, 6 May 2016
Introduction
Usage
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.
PGAP.pl -strains nickname1+...+nicknameN -input <input_dir> -output <out_dir> --cluster --pangenome --variation --evolution --function -method MP|GF
