Matrices

The following matrices are distributed with the scoring-matrices package and can be loaded with ScoringMatrix.from_name:

3DI

3di structural alphabet scoring matrix used in Foldseek.

Added in version 0.3.1.

BENNER6, BENNER22, BENNER74

Matrices proposed in Benner, Cohen and Gonnet (1994).

BLOSUM30, BLOSUM35, BLOSUM40, BLOSUM45, BLOSUM50, BLOSUM55, BLOSUM60, BLOSUM62, BLOSUM65, BLOSUM70, BLOSUM75, BLOSUM80, BLOSUM85, BLOSUM90, BLOSUM100, BLOSUMN

BLOcks SUbstitution Matrix series, computed by Henikoff (1992) from databases of local alignments. BLOSUM62 is the default matrix used in the BLAST algorithm.

DAYHOFF

An alias for the PAM-250 with additional B, Z, X and * scores.

GONNET

PAM 250 matrix recommended by Gonnet, Cohen & Benner (1992).

NUC.4.4

The extended DNA scoring matrix (sometimes also EDNAFULL) created by Todd Lowe (1992).

PAM10, PAM20, PAM30, PAM40, PAM50, PAM60, PAM70, PAM80, PAM90, PAM100, PAM110, PAM120, PAM130, PAM140, PAM150, PAM160, PAM170, PAM180, PAM190, PAM200, PAM210, PAM220, PAM230, PAM240, PAM250, PAM260, PAM270, PAM280, PAM290, PAM300, PAM310, PAM320, PAM330, PAM340, PAM350, PAM360, PAM370, PAM380, PAM390, PAM400, PAM410, PAM420, PAM430, PAM440, PAM450, PAM460, PAM470, PAM480, PAM490, PAM500

Point-Accepted Mutation matrix series computed by Dayhoff (1966).

VTML10, VTML20, VTML40, VTML80, VTML120, VTML160

Matrices computed with the resolvent method developed by Müller and Vingron to improve estimation of exchange frequencies. VTML80 is used by MMseqs2 for the k-mer generation process.