SimilarityMatrix

class pytrimal.SimilarityMatrix

A similarity matrix for biological sequence characters.

__init__(*args, **kwargs)

aa()

Create a default amino-acid similarity matrix (BLOSUM62).

distance(a, b)

Return the distance between two sequence characters.

Example

>>> mx = SimilarityMatrix.nt()
>>> mx.distance('A', 'A')
0.0
>>> mx.distance('A', 'T')
1.5184...

nt(degenerated=False)

Create a default nucleotide similarity matrix.

Parameters

degenerated (bool) – Set to True to create a similarity matrix for degenerated nucleotides.