This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Changing gap open and extension penalties in muscle (or any other command line tool that works on mac, really)

I'm trying muscle after learning that clustal omega doesn't allow for changing gap opening and extension scores. I am looking at the documentation, and I don't see a way of changing gap opening and extension scores (except for the termini, etc.). When I run the compiled executable on the command line, it prints out some options, which includes:

 Generate resampled ensemble from existing ensemble by sampling columns with replacement:
muscle -resample ensemble.efa -output resampled.efa

-maxgapfract F
   Maximum fraction of gaps in a column (F=0..1, default 0.5).

-minconf CC
   Minimum column confidence (CC=0..1, default 0.5).

I thus tried

muscle -align seqs.fasta -threads 6 -output test.fasta -maxgapfract 0.1

but I get an error message that says

Invalid command line
Unknown option maxgapfract

I'm surprised that this, in general, isn't a trivial thing to change. Am I using the wrong software? What command line tool I can compile on mac can allow me to change the gap open/extend scores?

Edit: I should also add that I'm trying to align proteins, but I'd like to be able to do this for dna sequences as well.

multiple-sequence-alignment
• 2,023 views • link
updated by erikatatianacs • erikatatianacs • written by sodiumnitrate • sodiumnitrate

1 answer

This may be a late answer, but this can help other users. I was having the same problem, and I spent a lot of time trying to figure the problem out, so: First, you make the alignment:

muscle3 -align input.fa -output aln.afa

And then, in the alignment file, you do the gap open penalty and the gap extension penalty.

muscle3 -in aln.afa -out aln_gap2_e1.afa -gapopen -2 -gapextend -1
• 0 views • link
written by erikatatianacs • erikatatianacs

Log in to answer this question.

More posts like this