Pan-Genome Analysis Web Server

A Better Way to Bacterial Pan-genome Analysis

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Blast off with Bootstrap

  • Orthologs clusters identification among multiple genomes
  • Pan-genome analysis for given strains
  • Functional genes variation and SNP calling among given strains
  • Evolutionary analysis based on pan-genome and SNP data
  • Orthologs clusters function analysis

    Complete genome or Draft genome


  • Genome Alignment for given strains
  • Orthologous gene identification for given strains
  • Genome variation analysis
  • Pan-genome analysis
  • Data visualization for gene distribution by conservation, genome structure and genetic variants

    Complete genome only



Support five analytic functions. Both dynamic visual figures and detailed pure text files are provided.

Easy to Use

Intutive and user-friendly interface, one-click setting of parameters and detailed users manual. Start first calculation within a minute.

Fast and Efficient

Calculation based on super computers of SCCAS, checking your tasks anytime and anywhere.


Please cite

  • PGAP: pan-genomes analysis pipeline. Bioinformatics,2012,28(3):416-8. [PMID= 22130594]
  • PanGP: a tool for quickly analyzing bacterial pan-genome profile. Bioinformatics,2014,30(9):1297-9. [PMID= 24420766]
  • PGAP-X: Extension on pan-genome analysis pipeline. BMC Genomics,2018,19(Suppl 1):36.[PMID= 29363431]
  • PGAweb: A Web Server for Bacterial Pan-Genome Analysis. Front Microbiol,2018,9:1910.[PMID= 30186253]