Table 1.

Results from analyses of five other data sets. For each data set is shown: the numbers of sequences in the alignment, the number of sites in the alignment, the optimal models of SE identified using ModelFinder and IQ-TREE’s implementations of jModelTest⁹ and ProtTest¹⁰ (Other Methods), and the differences in terms of the ∆BIC score and RF distance between phylogenetic estimates inferred using these optimal models of SE.

Data type, source & origin	Sequences	Sites	ModelFinder	BIC	Other Methods	BIC	∆BIC	RF
DNA, Lassa virus7	179	3,186	SYM+R5	131,325	SYM+I+Γ4	131,540	215	16
DNA, mitochondrial, mammals3	274	7,370	GTR+R8	681,837	GTR+I+Γ4	684,469	2,632	16
DNA, nuclear, birds4	200	394,684	GTR+R8	18,891,706	GTR+I+Γ4	18,969,054	77,348	4
Protein, plastids, green plants5	360	19,449	JTT+F+R10	2,830,471	JTT+F+I+Γ4	2,838,957	8,486	4
Protein, nuclear, yeast6	23	634,530	LG+F+R7	25,629,204	LG+F+I+Γ4	25,638,043	8,839	0