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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..
BPGA Sourceforge Page.
BPGA HomePage.
It was recently published in Scientific Reports.
Any suggestions for further improving the tool are welcome.
COG is 2003 database with update on 2014. As of my knowledge it has not been updated since. So BPGA uses this only. You can use KAAS to re-annotate the fasta file.