I am currently working on the data of bacteria that have been moved from an environment to another, and then sequenced frequently. I am therefore looking at any tools that I could use to get data on the evolution of my functionnal genomes, as I am relatively inexperienced in bioinformatics. So far, I already looked at prophages and mobile elements. For example, if I could have for each genome a quantification of each GO category of my genome, then I could see what GO terms have progressed and regressed over time, but I didn't manage to find tools to do that easily. I'll take any piece of advice !
Thank you in advance,