Table 1.

Numbers of parameters required by models of orders 1–5

Order	REV+JOINT	REV+JOINT+INDEP	GTR+COND+DUAL	GTR+COND+SINGLE	HKY+COND+SINGLE	FEL+COND+SINGLE
1	120	48	96	24	8	4
2	2016	288	1536	96	32	16
3	32 640	1536	24 576	384	128	64
4	523 000	7680	393 216	1536	512	256
5	8×106	36 864	6×106	6144	2048	1024

GTR: reversible 4×4 model (six parameters + equilibrium frequencies) of Tavaré (1986); REV: general reversible model on n-mers of any size; JOINT: utilizes a single joint matrix; COND: utilizes a collection of conditional matrices; DUAL: assumes dual contexts; SINGLE: assumes single contexts; INDEP: assumes multiple changes in an n-mer are conditionally independent; HKY: Hasegawa et al. (1985) model (two parameters + equilibrium frequencies); FEL: Felsenstein's (1981) model (one parameter + equilibrium frequencies).