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Table 4 The optimal parameters for each data set

From: Determination of optimal parameters of MAFFT program based on BAliBASE3.0 database

Data set

The optimal substitution matrix

The best MAX_MEAN_SPS value

The optimal GOP

The optimal of GEP

RV11

Blosum45

0.5912

2

0.12

RV12

Blosum45

0.8465

2.9

1.44

RV20

Blosum62

0.8594

2.3

0.63

RV30

Blosum62

0.7819

2.1

0.72

RV40

Blosum45

0.6818

2.8

0.39

RV50

Blosum45

0.7505

2.8

0.03