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Prograns to idIdentify core genes under negative selection
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?
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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...
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