Question: PIM from MUSCLE
0
gravatar for vdjonsson
3.1 years ago by
vdjonsson0
vdjonsson0 wrote:

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.

ADD COMMENTlink modified 3 months ago by gadget0 • written 3.1 years ago by vdjonsson0

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

ADD REPLYlink written 5 months ago by bjoern.pietzenuk0
0
gravatar for gadget
3 months ago by
gadget0
gadget0 wrote:

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

ADD COMMENTlink written 3 months ago by gadget0
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