TABLE 3.

Evaluation of the congruence between phylogenetic trees obtained using nucleotide sequences of clonal viruses from different regions of the viral genome^a

Regions being comparedb	P value for each comparison for the indicated patient
	1	2	3	4	5	6
gag + protease versus RT	0.044	0.135	0.004	0.002	0.001	0.001
Protease versus RT	0.115	0.936	0.013	0.146	0.001	0.005
gag-pol versus env C1-V4	0.001	0.001	0.022	0.003	0.001	0.001

^aPhylogenetic trees for the indicated genomic regions were generated using the maximum likelihood method and were compared using the incongruence length difference test. For each patient, P values for each comparison are shown; a P value of <0.05 (boldface type) indicates that the phylogenetic trees were not congruent.

^bThe nucleotide sequences used to generate trees were as follows: gag + protease, 1930 to 2549; RT, 2670 to 3308; protease, 2253 to 2549; gag-pol, 1930 to 3308; env C1-V4, 6221 to 7567.