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

BMC Bioinformatics

Table 5 Clustering results for the Gap Procedure on HIV-1 data

Subset	Time (in sec)	1 ✓	1 ✗	2–4	≥5	ARI
all	10.56 sec	237	16	244 (619)	61 (645)	0.9170
men	8.261 sec	225	18	215 (536)	60 (612)	0.9097
non.sing	3.086 sec	–	12	125 (351)	57 (621)	0.9325
nsm	2.470 sec	–	11	109 (303)	54 (589)	0.9320
big	0.807 sec	–	3	5 (14)	61 (656)	0.9523
mibc	0.634 sec	–	3	5 (14)	56 (610)	0.9492

The ARI scores and running times of the Gap Procedure when performed on subsets of the HIV-1 data. The number of correctly (and incorrectly) identified singletons are listed under “1\(\checkmark \)” (and “1✗”). The total number of for small and large-sized are listed under the headings (2–4) and (≥5). The corresponding number of sequences belonging to each class is given in parentheses

ISSN: 1471-2105