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I've written a little script to remove identical sequences from fasta to get what I need. To print the list of removed sequences, uncomment line 22 #! /usr/bin/python3 # Removes identical sequences from fasta file import sys from Bio import SeqIO sequences={} #This is where sequences will be stored #likely calling str(seq.seq) on every test will be slower ...


I'm not sure if there's a way on GenBank, but UniProt offers UniRef where you can cluster redundant sequences or specify a lower cutoff (like 90% identity).


Download the BLOSUM data and source-code from here. Unzip the archive which has several files. The file called blosum'XX'.qij will have the co-occurence probabilities, and the subsitution probabilities can be calculated from them. Also have a look at this article.

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