PIM from MUSCLE

Question

[vdjonsson]

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.

[bjoern.pietzenuk]

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

Answer 1

[gadget]

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