Table 2.

Overview of the datasets used in phylogenetic reconstructions

dataset	number of sequences	number of aa	alpha1	sequences with divergent aa composition2
hexokinase	28	263	0.98	Treponema denticola
glucose phosphate isomerase	40	431	0.78	Plasmodium falciparum Dictyostelium discoideum Aquifex aeolicus
fructose bisphosphate aldolase	25	268	0.67	Aquifex aeolicus
triose phosphate isomerase	31	211	0.62	Aquifex aeolicus Dictyostelium discoideum
glyceraldehyde phosphate dehydrogenase	40	271	0.64
phosphoglycerate kinase	34	277	0.67
phosphoglycerate mutase	37	394	0.86	Desulfovibrio vulgaris Gracilaria tenuistipitata Porphyra purpurea Encephalitozoon cuniculi Halobacterium sp.
enolase	33	336	0.70
pyruvate kinase	31	297	0.64	Giardia lamblia
pyruvate phosphate dikinase	29	682	0.51	Rickettsia prowazekii Thermobifida fusca

¹ the gamma shape parameter of the gamma distribution estimated using TREE-PUZZLE

² based on the chi square tests for deviation of amino acid frequencies implemented in TREE-PUZZLE