A PWM with gapped alignments in Biopython?

I use Perl, I see you are using Python, but the logic is basically the same. I use a system call to the clustal executable instead of using BioPerl/Biopython. I believe the clustalw2 executable handles gapped alignments without the need to call an alphabet.

Not 100 percent sure, but this is a script I use that works for me. Create a directory with all of your aligments files in it (I use . Fasta but you can change the flags on the system call to accept others).

This is my Perl script, you must modify the executable path in the last line to match clustal's location on your computer. Hope this helps a bit. As a side note, this is good for making many alignments very quickly, which is what I use it for but if you are only looking to align a few files, might want to skip the whole creating a directory and modify the code to accept a filepath and not a dirpath.

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