skbio.alignment.make_identity_substitution_matrix¶

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

Generate substitution matrix where all matches are scored equally

Note

Deprecated as of 0.4.0 for removal in 0.6.0. Will be replaced by a SubstitutionMatrix class. To track progress, see [#161](https://github.com/biocore/scikit-bio/issues/161).

Parameters
• match_score (int, float) – The score that should be assigned for all matches. This value is typically positive.

• mismatch_score (int, float) – The score that should be assigned for all mismatches. This value is typically negative.

• alphabet (iterable of str, optional) – The characters that should be included in the substitution matrix.

Returns

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.

Return type

dict of dicts