Results of CodeML analyses for the full alignment

CodeML parameter and result files

	M0	M1a	M2a	M7	M8	M8a
F3X4	results | params	results | params	results | params	results | params	results | params	results | params
F1X4	results | params	results | params	results | params	results | params	results | params	results | params
F61	results | params	results | params	results | params	results | params	results | params	results | params

Likelihood ratio tests between nested models

Green = LRT was significant at significance level 0.1

Red = LRT was not significant.

	M1a-M2a	M7-M8	M8a-M8
F61	lnL_M1a = -15065.89181 lnL_M2a = -15065.89181 LRT: χ2 = 0.0 % sites with ω > 1 = NA avg(ω) = NA p = 1.0	lnL_M7 = -15007.849384 lnL_M8 = -15003.594555 LRT: χ2 = 8.51 % sites with ω > 1 = 4.13 avg(ω) = 1.0 p = 0.014	lnL_M8a = -15003.594555 lnL_M8 = -15003.594555 LRT: χ2 = 0.0 % sites with ω > 1 = NA avg(ω) = NA p = 1.0
F1X4	lnL_M1a = -14727.03979 lnL_M2a = -14727.03979 LRT: χ2 = 0.0 % sites with ω > 1 = NA avg(ω) = NA p = 1.0	lnL_M7 = -14630.915246 lnL_M8 = -14624.79465 LRT: χ2 = 12.241 % sites with ω > 1 = 2.41 avg(ω) = 1.0 p = 0.002	lnL_M8a = -14624.79465 lnL_M8 = -14624.79465 LRT: χ2 = 0.0 % sites with ω > 1 = NA avg(ω) = NA p = 1.0
F3X4	lnL_M1a = -14606.582632 lnL_M2a = -14606.582632 LRT: χ2 = 0.0 % sites with ω > 1 = NA avg(ω) = NA p = 1.0	lnL_M7 = -14494.457545 lnL_M8 = -14485.147209 LRT: χ2 = 18.621 % sites with ω > 1 = 2.16 avg(ω) = 1.0 p < 0.001	lnL_M8a = -14485.147209 lnL_M8 = -14485.147209 LRT: χ2 = 0.0 % sites with ω > 1 = NA avg(ω) = NA p = 1.0