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