PGAP-X is a tool or so called "platform" for comparative genomics data analysis and viusalization, especially for procaryotic genomes. This tool integrates four functional modules including multi-sequence alignment("Genome Alignment"), orthologous gene identification("Orthologs Analysis"), genome variation analysis("Variation Analysis"), and pan-genome analysis("Pan-genome Analysis").

Genome alignment is the fundamental part of comparative genomics, this module is about local multi-sequence alignment, it can find ortholog regions in genomes. Orthologs analysis is based on result of genome alignment and genome annotation, it can identify ortholog clusters, and genes in one cluster is supposed to have the same ancestor, and may have the same function. Variation analysis contains genome region variation analysis and gene variation analysis, it can find SNP and InDel, taking genome region and gene as a unit. Pan-genome analysis can get the pan-genome profile, which will present the observed trends of pan-genome, core-genome and genome number.

PGAP-X also provides visualizing components respectively for each functional module.

At the same time, PGAP-X accepts other comparative genomics analyzing results imported by users and provides corresponding visualization results with powerful compatibility.

The advantage of PGAP-X over traditional comparative genomic tools are that this tool is compatible for major operation systems(Windows and Linux), it can be deployed conveniently on researcher's personal computers; it is easy to operate and can provide intuitional visualization results; it intergrates multiple functional modules and can carry out a comprehensive comparative genomics analysis.

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