Figure. Phylogenetic classification of env gp41 HIV-1 sequences from Ugandan (UG) patients (GenBank accession numbers for subtypes A and D are pending). Numbers before the abbreviation UG indicate the year of specimen collection; c1, c7, and c9 denote the UVRI, Mulago, and Nsambya clinics, respectively. The trees were constructed on the basis of 354-bp DNA sequences by the neighbor joining method with nucleotide distance datum sets calculated by Kimura's two-parameter approach and rerooted by using SIV-cpz as the outgroup. Arrows indicate reference subtype A and D sequences; asterisks indicate sequences, which decrease the bootstrap value from 90% to 73% in subtype A and from 85% to 55% in subtype D sequences. The scale bar indicates the evolutionary distance of 0.10 nucleotides per position in the sequence. Vertical distances are for clarity only. An automated DNA sequencer (Applied Biosystems Model 373, Foster City, CA) was used to generate sequence data for alignment with the CLUSTAL version V multiple sequence alignment program and subsequent phylogenetic analysis. Phylogenetic relationship of sequences was analyzed by the neighbor joining method (PHYLIP package version 3.5c with and without bootstrapping), and the maximum-likelihood method (fastDNA program, version 1.0.8, which uses randomized data input and global rearrangement). The stability of tree topology was tested by pruning, which consisted of removing one species from the alignment and rerunning the phylogenetic analysis. Accurate subtype determination using env gp41 has been shown to be similar to that based on env C2V3 sequences (22). The gp41 DNA sequences Environment package, and immunodominant regions were analyzed (23). The reference sequences for subtypes A-J, groups O and N, and SIVcpz were retrieved from the 1997 HIV-1 Molecular Immunology Database (Los Alamos National Laboratory, Los Alamos, NM).