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.
Question: PIM from MUSCLE
3.1 years ago by
vdjonsson • 0
vdjonsson • 0 wrote:
ADD COMMENT • link •
3 months ago by
gadget • 0
gadget • 0 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 COMMENT • link
Please log in to add an answer.
Powered by Biostar version 2.3.0
Traffic: 2032 users visited in the last hour