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

BMC Bioinformatics

Table 2 Clustering results for RAxML on simulated data

	Sim	T _c	T _d	Time (in sec)	# clusters	# singletons	ARI
RAxML	1	90	0.3	2479.0	13	21	0.3662
	2	90	0.3	4654.0	13	10	0.7054
	3	90	0.3	41584.6	61	33	0.6206
	4	90	0.3	271593.7	167	70	0.4889
	1	90	0.6	2479.0	7	4	0.8757
	2	90	0.6	4654.0	9	5	0.8945
	3	90	0.6	41584.6	24	6	0.9764
	4	90	0.6	271593.7	54	2	0.9922

The clustering results (for a single run) obtained by RAxML when applied to the simulated data. The quoted run times represent the time it takes RAxML to produce a phylogenetic tree and obtain clade support values (conducted using 100 bootstrap replicates). RAxML 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