Hi Agnieska.
Following our conversation about matrices - either hard-coded or stored in files, I finally found the relevant web site I was trying to locate with regard to text file representation of matrices.
The web site is the 'AAindex' database:
http://www.genome.jp/aaindex/
Here's the BLOSUM62 matrix as an aaindex file:
http://www.genome.jp/dbget-bin/www_bget?aaindex:HENS920102
Jim.
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