Supplementary Data 1. Position of all identified mutations in the env gene. This file contains detailed information about the identity of the observed mutations. It provides the position in the HXB2 genome, the amino acid change they cause in the different genetic backgrounds and the number of HIV-1 subtypes (out of a total of 170) the mutations occurs in. Supplementary Data 2. Position of all identified mutations in the rev exon part of the env gene. Same as Supplementary Data 1, except that only mutations and amino acid substitutions in the rev exon 2 are shown. Supplementary Program. With this program one can redo the analyses and simulations of the manuscript.