Phylogenetic analysis of gag and env genes. Bayesian inference trees were generated for the first ~1800 bp of gag (A), as well as the SU portion of env (B). Trees were rooted using the 17p13.1 provirus sequence as an out-group, with posterior probabilities above 80 shown. Sequences are color-coded according to LTR group, with type 1 proviruses indicated with filled diamonds, and undetermined types with open diamonds. All other proviruses shown are type 2.