I have 20 genomes (Whole genome sequencing) obtained from illumina and assembled with Spades, so I want to compare the differences among tow groups (each group have 10 genomes), and determinate the differences among groups in terms of gene ontology. The Patric web server generate a code like: GO:0004823|leucine-tRNA ligase activity, base in the assembled contigs, but the problems is that not all genes have a GO term, so I was wonder if it is any webserver, or any command line tool (if it is in R, much beater) to determinate the differences among tow groups of genomes based in GO term.... it there some papers ( Pyrosequencing-Based Comparative Genome Analysis of Vibrio vulnificus Environmental Isolates ), but the pipeline is not clear for me !!! if you have any pipeline of any suggestion let me know !!!