Table 3.
Existing amino-acid replacement matrices
| Matrix | Reference | Genomic regions |
|---|---|---|
| Blosum62 | Henikoff and Henikoff (1992) | General |
| Dayhoff | Dayhoff et al. (1978) | General |
| JTT | Jones et al. (1992) | General |
| LG | Le and Gascuel (2008) | General |
| PMB | Veerassamy et al. (2003) | General |
| VT | Muller and Vingron (2000) | General |
| WAG | Whelan and Goldman (2001) | General |
| mtArt | Abascal et al. (2007) | Mitochondrial |
| mtMam | Yang et al. (1998) | Mitochondrial |
| mtRev | Adachi and Hasegawa (1996) | Mitochondrial |
| mtZoa | Rota-Stabelli et al. (2009) | Mitochondrial |
| mtMet | Le et al. (2017) | Mitochondrial |
| mtVer | Le et al. (2017) | Mitochondrial |
| mtInv | Le et al. (2017) | Mitochondrial |
| cpRev | Adachi et al. (2000) | Chloroplast |
| FLU | Cuong et al. (2010) | Viral |
| HIVb | Nickle et al. (2007) | Viral |
| HIVw | Nickle et al. (2007) | Viral |
| rtREV | Dimmic et al. (2002) | Viral |