Models of Evolution

Nucleotide substitution models

Model	Reference	d.f.	Base freq	Symmetries	code
JC	Jukes and Cantor 1969	0	equal	AC=AG=AT=CG=CT=GT	000000
F81	Felsenstein, 1981	3	unequal	AC=AG=AT=CG=CT=GT	000000
K80	Kimura, 1980	1	equal	AC=AT=CG=GT AG=GT	010010
HKY	Hasegawa et al., 1985	4	unequal	AC=AT=CG=GT AG=GT	010010
TrNef	Tamura and Nei, 1993	2	equal	AC=AT=CG=GT AG GT	010020
TrN	Tamura and Nei, 1993	5	unequal	AC=AT=CG=GT AG GT	010020
TPM1 (K81)	Kimura, 1981	2	equal	AC=GT AG=CT AT=CG	012210
TPM1uf	Kimura, 1981	5	unequal	AC=GT AG=CT AT=CG	012210
TPM2		2	equal	AC=AT CG=GT AG=CT	010212
TPM2uf		5	unequal	AC=AT CG=GT AG=CT	010212
TPM3		2	equal	AC=AT AG=GT AG=CT	012012
TPM3uf		5	unequal	AC=CG AT=GT AG=CT	012012
TIM1	Posada, 2003	3	equal	AC=GT AT=CG AG CT	012230
TIM1uf	Posada, 2003	6	unequal	AC=GT AT=CG AG CT	012230
TIM2		3	equal	AC=AT CG=GT AG;CT	010232
TIM2uf		6	unequal	AC=AT CG=GT AG;CT	010232
TIM3		3	equal	AC=CG AT=GT AG CT	012032
TIM3uf		6	unequal	AC=CG AT=GT AG CT	012032
TVMef	Posada, 2003	4	equal	AC CG AT GT AG=CT	012314
TVM	Posada, 2003	7	unequal	AC CG AT GT AG=CT	012314
SYM	Zharkikh, 1994	5	equal	AC CG AT GT AG CT	012345
GTR (REV)	Tavaré. 1986	8	unequal	AC CG AT GT AG CT	012345

Amino acid replacement models

1. Dayhoff (Dayhoff et al., 1978)
2. LG (Le and Gascuel, 2008)
3. DCMut (Kosiol and Goldman, 2005)
4. JTT (Jones et al., 1992)
5. mtREV (Adachi and Hasegawa, 1996)
6. WAG (Whelan and Goldman, 2001)
7. RtREV (Dimmic et al., 2002)
8. CpREV (Adachi and Waddell, 2000)
9. VT (Muller and Vingron 2000)
10. Blosum62 (Henikoff and Henikoff, 1992)
11. MtMam (Cao et al., 1998)
12. MtArt (Abascal et al., 2007)
13. MtZoa (Rota-Stabelli et al., 2009)
14. PMB (Veerassamy, Smith and Tillier, 2003)
15. HIVb (Nickle et al. 2007)
16. HIVw (Nickle et al. 2007)
17. JTT-DCMut (Kosiol and Goldman, 2005)
18. FLU (Dang et al., 2010)
19. StmtREV (Liu et al., 2014)