I want to use sequence alignments found by Foldseek in PROSS. I know there are other ways to get alignments (also tried with results of HHPred), but I had in mind that Foldseek may find remote homologs that would still be structurally relevant.

Currently Foldseek only gives alignment results in m8 format, however PROSS only accepts FASTA alignment files.

I tried looking into BioPython but it seems it doesn't open m8 files, only m9. I also tried importing the alignment in Clustal X but it can't read it.

I could probably use Foldseek CURL API to get the alignment as json and make a script to write the results in FASTA format, but this seems like a heavy handed solution.

What would be other tools I could try to convert m8 to FASTA?



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