BPGA is a fast pan-genome analysis tool for microbial genomes. Along with regular pan genome profiles, BPGA also provides detailed statistics and sequences with their downstream analysis like KEGG/COG assignments and phylogeny based on core, MLST as well as pan genome. In addition, it also studies genes with extreme/atypical GC contents as that of the genomic GC content, sub-grouping of large datasets etc..
It was recently published in Scientific Reports.
Any suggestions for further improving the tool are welcome.