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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?

  • #2
    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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