Changing gap open and extension penalties in muscle (or any other command line tool that works on mac, really)

Question

[sodiumnitrate]

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.

Answer 1

[erikatatianacs]

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