Maximum-likelihood tree for HIV-1 sequences from the patients studied.

<p>Shown are the maximum-likelihood phylogenies of viral nucleotide sequences from the Gag and Vif genes of HIV-1 derived from the ten patients at two time points during infection rooted with the estimated ancestral subtype B sequence <a href="http://www.plospathogens.org/article/info:doi/10.1371/journal.ppat.1004281#ppat.1004281-Korber2" target="_blank">[43]</a>. The sequences from each patient are individually colored and labeled accordingly. The maximum-likelihood tree shows viral sequences that belong to a transmission pair (S004 and S005) and a dually infected patient (S007). Branch lengths indicate the number of nucleotide substitutions per site. The scale bar at the bottom refers to the degree of sequence mismatch. Maximum-likelihood bootstraps are presented below each branch.