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 |
| − | * pan-genome profile | + | * ascertain pan-genome profile |
| − | * genetic variation | + | * genetic variation of functional genes |
* species evolution analysis | * species evolution analysis | ||
| − | * function enrichment | + | * function enrichment of gene clusters |
| − | The following commands | + | Example command for this stage: |
| − | 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 | ||
Revision as of 15:46, 6 May 2016
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
