PQ, a new program for phylogeny reconstruction

BMC Bioinformatics

Table 6 Numbers of “good” reconstructions

Dataset	Threshold	PQ	ME	ML	MP	QP
Metazoa-10	0.143	192	145	152	111	166
Metazoa-15	0.25	297	267	253	129	262
Fungi-15	0.167	166	143	108	71	161
Proteobacteria-15	0.417	143	126	81	71	127
Metazoa-25	0.273	188	169	173	61	147
Fungi-30	0.296	206	208	182	96	185
Proteobacteria-30	0.593	186	166	127	78	163
Fungi-45	0.357	198	236	211	108	187
Proteobacteria-45	0.643	152	134	110	57	128

The column “Threshold” contains first quartils of Robinson – Foulds distances between PQ trees and species trees, for each set. Numbers in other columns are numbers of trees reconstructed by each method whose distance to the corresponding species tree is less than the threshold. Numbers in PQ column are less than 1/4 of total volumes of the sets because the distance can take only few possible values

ISSN: 1471-2105