PQ, a new program for phylogeny reconstruction

BMC Bioinformatics

Table 11 Results of the programs on 500 simulated amino acid alignments

Value	PQ	ME	ML	MP	QP
<D>	0.144	0.165	0.111	0.133	0.136
r _DL	− 0.34	− 0.49	− 0.50	− 0.48	− 0.52
Perfect	15	13	65	24	19
Good	156	115	316	181	172
Bad	106	146	30	96	96
PQ is better	NA	248	53	167	188
PQ is worse	NA	145	347	227	198
P-value	NA	2·10⁻⁷	5·10⁻⁵⁴	0.003	0.65

The row <D> contains average Robinson – Foulds distances between inferred trees and reference trees. “Good” are numbers of inferred trees whose distance from the corresponding reference trees is less than 0.074. “Bad” are numbers of inferred trees whose distance from the corresponding reference tree is greater than 0.185. Other notations are the same as in Table 9

ISSN: 1471-2105