I am trying to align two fasta files with multiple sequences. The idea would be to use a sliding window approach, as done on this site: http://www.allermatch.org/allermatch.py/form
I want to use the same 80aa sliding window, and find all alignments with greater than 35% identity. Finally, I would like an overall identity score the aligned sequences.
I've tried BLAST, FASTA36, and DIAMOND so far. None of them have the 'sliding window' option. I even tried adjusting 'word sizes' in BLAST but no luck yet.
Any ideas on how one can pursue this?