Table 3.

Numbers of the free parameters for the fitted models

	Substitution model	Edge lengths
Model name	GTR1 + GTR2	Tree1 + Tree2	Class weights	Total
	(or one GTR for M-LGP)	(or one tree for P-LEL)
P-LEL	8 + 9	13	NA	30
P-UEL	8 + 8	13 + 13	NA	42
M-UGP	8 + 8	13 + 13	1	43
M-LGP	8	13 + 13	1	35

For the P-LEL model, one GTR model has 8 free parameters, but another GTR model has 9. This is because the P-LEL model shares the same edge lengths, and we cannot distinguish the times and the substitutional rates. Therefore, for the P-LEL model, if the rate of $G\to T$ in the substitution rate parameters of a GTR model is set to one, then the rate of $G\to T$ in the other GTR model need not be set to 1.