Quartet-based methods to reconstruct phylogenetic networks

BMC Systems Biology

Table 2 Comparison of true and reconstructed splits and weights on the artificial network 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	1.08	100	ab	1.09	100	ab	1.12	100	ab	1.08	100	ab	0.76	80	ab	0.41	56
abc	4	abc	4	100	abc	4	100	abc	4	100	abc	4	100	abc	4	100	abc	4	100
abd	1	abd	1.03	100	abd	1.03	100	abd	1.03	100	abd	1.02	100	abd	1.32	50
abcd	4	abcd	3.99	100	abcd	3.99	100	abcd	3.99	100	abcd	3.99	100	abcd	4.17	100	abcd	3.97	100
abce	1	abce	1.01	100	abce	1.02	100	abce	1.01	100	abce	1.01	100	abce	0.86	46
abcg	1	abcg	1.03	100	abcg	1.03	100	abcg	1.03	100	abcg	1.02	100	abcg	0.89	54
aefg	1	aefg	1.02	100	aefg	1.03	100	aefg	1.02	100	aefg	1.02	100	aefg	1.39	50
abcde	1	abcde	1.08	100	abcde	1.09	100	abcde	1.12	100	abcde	1.07	100	abcde	0.76	67	abcde	0.39	46
abcdg	1	abcdg	1.07	100	abcdg	1.08	100	abcdg	1.11	100	abcdg	1.07	100	abcdg	0.71	68	abcdg	0.39	54
abceg	2	abceg	2.07	100	abceg	2.09	100	abceg	2.12	100	abceg	2.07	100	abceg	2.36	47
acefg	2	acefg	2.06	100	acefg	2.07	100	acefg	2.11	100	acefg	2.06	100	acefg	2.23	8
adefg	1	adefg	1.08	100	adefg	1.09	100	adefg	1.12	100	adefg	1.07	100	adefg	0.76	73	adefg	0.43	44
a	10	a	10.31	100	a	10.15	100	a	10.17	100	a	10.43	100	a	10.07	100	a	9.42	100
b	6	b	6.25	100	b	6.11	100	b	6.07	100	b	6.33	100	b	7.62	100	b	7.15	100
c	10	c	10.26	100	c	10.11	100	c	10.12	100	c	10.38	100	c	10.05	100	c	9.40	100
d	4	d	4.21	100	d	4.06	100	d	4.08	100	d	4.26	100	d	6.02	100	d	6.82	100
e	10	e	10.28	100	e	10.14	100	e	10.16	100	e	10.41	100	e	10.12	100	e	9.43	100
f	6	f	6.25	100	f	6.11	100	f	6.06	100	f	6.34	100	f	7.22	100	f	7.11	100
g	10	g	10.31	100	g	10.16	100	g	10.18	100	g	10.44	100	g	10.14	100	g	9.47	100
											ac	0.08	99	abdfg	0.04	15
											abcdf	0.08	97	ag	0.04	13
											acdeg	0.02	74	ae	0.03	12
											acdef	0.03	66	abdef	0.04	10
											ae	0.04	65
											abdeg	0.03	65
											ag	0.04	64
											abdfg	0.04	64
											acdfg	0.02	62
											abdef	0.04	59
											af	0.03	58

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