Table 2.

A summary of the average Qfit and RF similarity scores between the four suggested phylogenies and the entire gene pool/NUTs.

	Similarity measure
	Qfit, entire gene pool	Qfit, NUTs	RF similarity, entire gene pool	RF similarity, NUTs
QP1 tree	0.315	0.566	0.418	0.413
QP2 tree	0.315	0.568	0.420	0.422
COG tree	0.285	0.524	0.393	0.348
Ribosomal protein tree	0.313	0.549	0.421	0.420

Specifically, the first row presents, from left to right, (1) the average Qfit between QP1 and the genes in the entire gene pool, (2) the average Qfit between QP1 and the NUTs, (3) The average RF between QP1 and the genes in the entire gene pool, (4) the average RF between QP1 and the NUTs. Similarly for the other three rows. the scores relating to the QP2 tree are highest in all categories but one (namely, RF with respect to the entire gene pool), where the scores of the QP2 tree and of the ribosomal protein tree are almost identical.