Viral Phylodynamics
Figure 6
Between-host and within-host HIV phylogenies.
Sequences were downloaded from the LANL HIV sequence database (http://www.hiv.lanl.gov/content/sequence/HIV/SI_alignments/set1.html). Neighbor-joining trees were estimated from Alignment1, and the within host tree is based on data from patient 2. Trees were re-rooted using Path-o-gen using known sample dates (http://tree.bio.ed.ac.uk/software/pathogen/).