Prograns to idIdentify core genes under negative selection

[correlimos]

I got multiple genomes for different gram-negative bacteria. What program could I use to identify specific core genes under negative selection but with smaller regions that exhibit positive selection? Is there any limitations/problems I might encounter along the way?

[SylvainL]

Do you have annotated genomes? Or just the assemblies?

If you have annotations, your project is quite similar to one project I'm working on right now...

My strategy is:
blast all genes vs each other
use R to look for gene clusters (then, you can apply the thresholds you want to decide whether a cluster has to be reported or not...)

If you don't have annotations, I would do more or less the same, instead that I would first try to make annotations using a software like glimmer...