Table 2.

Aggregate SPR distance to supertrees constructed from different rootings of the bacterial protein trees

MRP Rooted Gene Trees	SPR-Aquificae Rooted Gene Trees
	SPR Distance		SPR Distance
SPR–MRP-Rooting	52,867	SPR-Aquificae-Rooting	53,534
SPR–MRP	52,896	SPR-Aquificae	54,488
MRP	52,896	40-Aquificae	55,570
SPR-Aquificae-Rooting	58,539	SPR–MRP-Rooting	58,023
SPR-Aquificae	59,561	SPR–MRP	58,057
40-Aquificae	60,611	MRP	58,057

Notes: Six different construction methods were compared: The MRP supertree (MRP), the SPR supertree constructed from the 40 largest trees with a monophyletic Aquificae group (40-Aquificae), the SPR supertrees constructed using the MRP supertree (SPR–MRP) or SPR-Aquificae supertree (SPR-Aquificae), and the SPR supertrees constructed by only rooting the gene trees using the MRP supertree (SPR–MRP-Rooting) or SPR-Aquificae tree (SPR-Aquificae-Rooting) and building a greedy addition supertree. Each supertree was compared with the MRP rooted gene trees or SPR-Aquificae rooted gene trees with the SPR distance.