PIM from MUSCLE
I am trying to retrieve the percent identity matrix for a pairwise alignment in MUSCLE via a command line argument. When using the online tool, this result is specified under "results summary". It's not clear to me how to output this data from the command line.
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Biostar
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vdjonsson •
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vdjonsson •
1 answer
CLUSTAL-OMEGA can take the MUSCLE alignment as an input file to generate the PIM.
Run the following MUSCLE command line to generate a CLUSTALW alignment:
muscle -in input.fasta -clwstrictout aligned.clw
Then run CLUSTALO as follows:
clustalo -i aligned.clw --percent-id --distmat-out=pim.txt --full --force
For more examples see http://clustal.org/omega/README
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2.5 years later I have the exact same qestion! Anyone who knows the answere yet???