With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed. We have developed a new pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. PGAP's performance has been evaluated on 11 Streptococcus pyogenes strains.PGAP is developed with Perl script on the Linux Platform and the package is freely available from http://pgap.sf.net.junyu@big.ac.cn; xiaojingfa@big.ac.cnSupplementary data are available at Bioinformatics online.

PGAP: pan-genomes analysis pipeline