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 t