PGAP 1.2.1 / PGAP-X 1.0.4 / PGAweb – Pipeline for Pan-genome Analysis

PGAP 1.2.1 / PGAP-X 1.0.4 / PGAweb


PGAP (pan-genome analysis pipeline) 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-X is a microbial comparative genomic analysis platform with graphic interface.

PGAweb is a webserver for bacterial pan-genome analysis. It had integrated our previous published stand-alone tools PGAP, PanGP and PGAP-X into one server and simplifies the analysis of pan-genome.


Beijing Institute of Genomics, Chinese Acadamy of Sciences , Yongbing Zhao



  • Linux
  • Perl





Chen X, Zhang Y, Zhang Z, Zhao Y, Sun C, Yang M, Wang J, Liu Q, Zhang B, Chen M, Yu J, Wu J, Jin Z, Xiao J.
PGAweb: A Web Server for Bacterial Pan-Genome Analysis.
Front Microbiol. 2018 Aug 21;9:1910. doi: 10.3389/fmicb.2018.01910. PMID: 30186253; PMCID: PMC6110895.

Zhao Y, Sun C, Zhao D, Zhang Y, You Y, Jia X, Yang J, Wang L, Wang J, Fu H, Kang Y, Chen F, Yu J, Wu J, Xiao J.
PGAP-X: extension on pan-genome analysis pipeline.
BMC Genomics. 2018 Jan 19;19(Suppl 1):36. doi: 10.1186/s12864-017-4337-7. PMID: 29363431; PMCID: PMC5780747.

Bioinformatics. 2012 Feb 1;28(3):416-8. doi: 10.1093/bioinformatics/btr655. Epub 2011 Nov 29.
PGAP: pan-genomes analysis pipeline.
Zhao Y1, Wu J, Yang J, Sun S, Xiao J, Yu J.