I am comparing a large number of microbial genomes obtained from a complex microbial community. I performed the main functional annotations for the genes (COG, KEGG, Pfam) and I would perform a statistical analysis to classify genomes on the basis of their functional characteristics (i.e. identification of genomes enriched in specific functional categories). I have seen that some software perform similar analysis on metagenomes (i.e. Fantom). Can anyone suggest a tool to perform this analysis on genomes?
Thank you