Table 1.

The baseline setting

Parameter	Value
expected length L = 1/μ:	50
expected coverage P = ν/μ + ν):	0.25
background probability π:	A	C	G	T
	0.24034	0.25518	0.26097	0.24351
	A	C	G	T
substitution rate matrix Q (type:REV):	-1.02446	0.23112	0.58662	0.20672	A
	0.21767	-0.99759	0.20665	0.57327	C
	0.54024	0.20206	-0.95781	0.21551	G
	0.20402	0.60073	0.23095	-1.03570	T
un-rooted branch length β:	dog	human	mouse	rat	middle
	0.56496	0.33361	0.09604	0.10016	0.35807
conservation ratio ρ:	0.32

The table provides the fitted phylo-HMM parameter values (median values) from the alignments of orthologous promoters of dog, mouse, rat, and human. MLAGAN was used to align the orthologous promoters. Each promoter alignment of the 8533 orthologous gene clusters was fitted separately by phylo-HMM using the REV model for the substitution rate matrix.