Question

PIM from MUSCLE

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7.5 years ago

vdjonsson • 0

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.

MUSCLE alignment identity matrix • 3.7k views

ADD COMMENT • link updated 3.7 years ago by Biostar 20 • written 7.5 years ago by vdjonsson • 0

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2.5 years later I have the exact same qestion! Anyone who knows the answere yet???

ADD REPLY • link 4.8 years ago by bjoern.pietzenuk • 0

score 0 · Answer 1 · 2019-09-07

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