Maximum likelihood trees indicating the phylogenetic relationships between 727 gag (A) and 628 nef (B) sequences of HIV-1. The trees were constructed from these sequences with 100 boostrap replicates following removal of recombinant sequence fragments by a blinded fully exploratory screen for recombination using RDP3. Black squares at the end of the branches represent the gag and nef sequences sampled from Cameroon in this study, while red squares represent intragene recombinant fragments in our samples. The gag tree was rooted using HIV-1 group N, O, P and SIV CPZ isolates, while the nef tree was rooted with HIV-1 group N, O and P isolates. Solid and open circles indicate branches with greater than 70% and 50% bootstrap support, respectively. The arrow in the nef tree indicates an outlier of both clades G and CRF02_AG.