TABLE 1

Maximum-likelihood estimated substitution parameters for constrained (clock) and unconstrained phylogenies inferred from the env and gag genes isolated from HIV-1 subtypes A and B

ParametersSubtype A env geneSubtype A gag geneSubtype B env geneSubtype B gag gene
Base frequencies πA, πC, πG, πT0.346, 0.175, 0.233, 0.2470.370, 0.188, 0.247, 0.1950.343, 0.174, 0.235, 0.2480.372, 0.189, 0.248, 0.191
Relative rate parametersa inferred from constrained phylogeny2.35, 4.55, 0.770, 0.750, 4.361.66, 6.98, 0.944, 0.663, 8.733.15, 5.70, 0.994, 1.16, 5.191.10, 3.58, 0.570, 0.298, 4.98
Gamma parameter, α, from constrained phylogeny0.3390.3500.2980.265
Relative rate parameters inferred from unconstrained phylogeny2.31, 4.58, 0.762, 0.807, 4.281.63, 6.80, 0.912, 0.653, 8.323.26, 5.86, 1.01, 1.27, 5.461.09, 3.76, 0.579, 0.333, 4.73
α from unconstrained phylogeny0.2910.3860.3230.240
  • a The five relative rate parameters of the general reversible model of nucleotide substitution (Lanave et al. 1984; Rodriguez et al. 1990) are in the order A → C, A → G, A → T, C → G, C → T, with G → T constrained to 1.0 (because parameters are relative to one another).