Table 1 MAFFT algorithms and parameters (substitution matrix is denoted by bl)
From: Determination of optimal parameters of MAFFT program based on BAliBASE3.0 database
Method types | Algorithms | Parameters | Explain |
|---|---|---|---|
Progressive methods | FFT-NS-1 | gop 1.53 gep 0.123 bl 62 retree 1–maxiterate 0 | Approximately two times faster than the default |
FFT-NS-2 | gop 1.53 gep 0.123 bl 62 retree 2–maxiterate 0 | The accuracy of the FFT-NS-2 is slightly higher than that of the FFT-NS-1 | |
Iterative refinement method | FFT-NS-i | gop 1.53 gep 0.123 bl 62 retree 2–maxiterate 1000 | Fastest in this category. Uses WSP score only |
NW-NS-i | gop 1.53 gep 0.123 bl 62 retree 2–maxiterate 0 | Distance is by the 6mer method | |
Iterative refinement methods using WSP and consistency scores | L-INS-i | gop 1.53 gep 0.123 bl 62 retree 2–maxiterate 1000–localpair | Uses WSP score and consistency score from local alignments |
E-INS-i | gop 1.53 gep 0.123 bl 62 retree 2–maxiterate 1000–genafpair | Uses WSP score and consistency score from local alignments with a generalized affine gap cost | |
G-INS-i | gop 1.53 gep 0.123 bl 62 retree 2–maxiterate 1000–globalpair | Uses WSP score and consistency score from global alignments |