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  • MUSCLE Alignment Stats

    Hey I posted previously on The Muscle Alignment thread but didn't get any response so I thought I would try a new thread. Does any one know how to output the percent identity for each alignment using the MUSCLE command line? or any other alignment stats?

    Thanks Leanne

  • #2
    As far as I know, the muscle command line tool doesn't provide the possibility to output anything like this. The only thing you could do is to use clustalw output from muscle (-clw) and parse it afterwards (# of asterisks (identical positions) / alignment length = percent identity)...

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