Molecular Biology and Evolution, Vol 16, 173-179, Copyright © 1999 by Society for Molecular Biology and Evolution
JM Koshi, DP Mindell and RA Goldstein
HIV-1 subtype phylogeny is investigated using a previously developed
computational model of natural amino acid site substitutions. This model,
based on Boltzmann statistics and Metropolis kinetics, involves an order of
magnitude fewer adjustable parameters than traditional substitution
matrices and deals more effectively with the issue of protein site
heterogeneity. When optimized for sequences of HIV-1 envelope (env)
proteins from a few specific subtypes, our model is more likely to describe
the evolutionary record for other subtypes than are methods using a single
substitution matrix, even a matrix optimized over the same data. Pairwise
distances are calculated between various probabilistic ancestral subtype
sequences, and a distance matrix approach is used to find the optimal
phylogenetic tree. Our results indicate that the relationships between
subtypes B, C, and D and those between subtypes A and H may be closer than
previously thought.
ORIGINAL ARTICLE
Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes
Biophysics Research Division, University of Michigan, Ann Arbor 48109- 1055, USA.
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