HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences

Simulation studies were conducted to characterise the implications of missing nucleotide characters in PANGEA-HIV sequences on tree reconstruction accuracy. An individual-level transmission model was used to generate regional HIV-1 epidemics, as well as corresponding HIV-1 phylogenies and full genome sequences. Each simulated sequence was paired at random with a PANGEA-HIV sequence, and missing nucleotide patterns of PANGEA-HIV sequences were superimposed onto the simulated sequences. This data contains the simulated sequence alignments, and might be useful to benchmark tree reconstruction tools.