Quartet-based methods to reconstruct phylogenetic networks

BMC Systems Biology

Table 1 Comparison of true and reconstructed splits and weights on the artificial tree by 6 methods

True Phylo		QuartetS			QuartetA			QuartetM			Quartet-Net			Neighbor-Net			Neighbor-Joining
Split	Wei	Split	Wei	BV	Split	Wei	BV	Split	Wei	BV	Split	Wei	BV	Split	Wei	BV	Split	Wei	BV
ab	1	ab	1	100	ab	1	100	ab	1	100	ab	1	100	ab	1	100	ab	1	100
abcd	3	abcd	3.03	100	abcd	3	100	abcd	2.98	100	abcd	3.03	100	abcd	2.98	100	abcd	2.98	100
abef	1	abef	1.03	100	abef	1.03	100	abef	1.03	100	abef	1.03	100	abef	1.02	100	abef	1.02	100
a	1	a	1.03	100	a	0.99	100	a	0.98	100	a	1.03	100	a	1.04	100	a	1.04	100
b	1	b	1.04	100	b	1	100	b	0.99	100	b	1.04	100	b	1.05	100	b	1.05	100
c	1	c	1.03	100	c	0.99	100	c	0.98	100	c	1.03	100	c	1.04	100	c	1.04	100
d	1	d	1.03	100	d	0.99	100	d	0.98	100	d	1.03	100	d	1.04	100	d	1.04	100
e	1	e	1.04	100	e	1.01	100	e	1.00	100	e	1.04	100	e	1.04	100	e	1.05	100
f	1	f	1.06	100	f	1.03	100	f	1.02	100	f	1.06	100	f	1.06	100	f	1.06	100
											abc	0.01	15	abc	0.02	31
											abd	0.02	15	abd	0.02	40
											acef	0.01	15	acef	0.01	21
														abf	0.02	34
														acd	0.02	33
														aef	0.02	36
														abe	0.02	35
														ad	0.01	16
														ae	0.01	15
														adef	0.01	19

The column “True Phylo” denotes the underlying truth and the columns “QuartetS”, “QuartetA”, “QuartetM”, “Quartet-Net”, “Neighbor-Net”, and “Neighbor-Joining” denote the reconstructed results by each method respectively. In addition, “Wei” denotes the average weight of the corresponding split over 100 runs; “BV” denote bootstrap value.

ISSN: 1752-0509