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.

Deprecated since version 0.4.0: It has been replaced by the SubstitutionMatrix class. Additional details at: scikit-bio/scikit-bio#1913.

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.