Fast NJ-like algorithms to deal with incomplete distance matrices

BMC Bioinformatics

Table 4 Run times

(a): 25% taxon deletion rate
	SDM		FITCH			MW*			MVR*
	K =		k =			k =			k =
	10	2	10	20	2	10	20	2	10	20
n = 48	< 1	11	23	23	21	39	41	< 1	< 1	< 1
n = 96	5	437	482	479	623	932	926	7	6	5
n = 192	32	11,065	13,864	13,945	23,541	34,368	35,017	57	60	42
(b): 75% taxon deletion rate
	SDM		FITCH			MW*			MVR*
	k =		k =			k =			k =
	10	2	10	20	2	10	20	2	10	20
n = 48	< 1	6	17	23	10	28	36	< 1	< 1	< 1
n = 96	< 1	22	455	492	29	656	667	< 1	4	7
n = 192	2	448	11,532	14,025	916	32,371	34,152	3	31	52
(c): 1.2% missing distances (Driskell et al.)
	SDM		FITCH			MW*			MVR*
	k = 254		k = 254			k = 254			k = 254
n = 48	334		132			268			< 1

Mean run times are provided for various taxon numbers (n), gene numbers (k) and proportions of missing entries: (a) 25%, (b) 75%, and (c) 1.2% using Driskell et al. [20]-like datasets. Run times are measured in seconds using a standard PC (Pentium IV 1.8 GHz, 1Gb RAM). The low run times with k = 2 and 75% deletion rate are explained by the low size of the distance super-matrices (see text for explanations).

ISSN: 1471-2105