skbio.alignment.make_identity_substitution_matrix

skbio.alignment.make_identity_substitution_matrix(match_score, mismatch_score, alphabet='ACGTU')

Generate substitution matrix where all matches are scored equally.

Parameters:

match_scoreint, float

The score that should be assigned for all matches. This value is typically positive.

mismatch_scoreint, float

The score that should be assigned for all mismatches. This value is typically negative.

alphabetiterable of str, optional

The characters that should be included in the substitution matrix.

Returns:

dict of dicts

All characters in alphabet are keys in both dictionaries, so that any pair of characters can be looked up to get their match or mismatch score.

Warning

make_identity_substitution_matrix is deprecated as of 0.4.0. It has been replaced by a SubstitutionMatrix class. Additional details at scikit-bio/scikit-bio#1913.