The Gap Procedure: for the identification of phylogenetic clusters in HIV-1 sequence data

BMC Bioinformatics

Table 3 Clustering results for MrBayes on simulated data

	Sim	T _c	T _d	Time (in sec)	# clusters	# singletons	ARI
MrBayes	1	90	0.3	3324.7	13	3	0.4642
	2	90	0.3	4243.6	19	7	0.5129
	3	90	0.3	144284.8	54	11	0.6565
	4	90	0.3	1328253.9	134	25	0.6269
	1	90	0.6	3324.7	8	2	0.8419
	2	90	0.6	4243.6	10	3	0.9011
	3	90	0.6	144284.8	24	6	0.9768
	4	90	0.6	1328253.9	52	3	0.9927

The clustering results (for a single run) obtained by MrBayes when applied to the simulated data. The quoted run times represent the time it takes MrBayes to estimate a phylogenetic tree with clade support (i.e., posterior probability) values. MrBayes clusters are obtained using a clade support threshold equal to T _c and distance thresholds of T _d. The ARI scores in bold indicate which runs performed better than the average score obtained using the Gap Procedure

ISSN: 1471-2105