Scheme | Size | Matrix | Gaps# | Reference |
---|
ML* | 4,8,10,15 | BL50 | 12/2 | [28] |
EB§ | 13,11,9,8,5 | BL62 | 11/1 | [18] |
HSDM* | 17 | HSDM | 19/1 | [29] |
SDM* | 12 | SDM | 7/1 | [29] |
GBMR* | 4 | BL62 | 11/1 | [30] |
RANDOM§ | 4,4,4 | BL62 | 11/1 | This study |
- Reduced amino acid schemes used in this study.* Substitution matrices for these reduced alphabets were obtained from reference [33]. § BL62 frequency counts were used to derive these substitution matrices using the formula outlined in reference [33]. #Gap opening/gap extension penalties used for MSAs in ClustalW2.