Diverse phylogenetic methods require a substitution model of evolution that should mimic,
as accurately as possible, the real substitution process. At the protein level, empirical …

Substitution models of evolution are necessary for diverse evolutionary analyses including
phylogenetic tree and ancestral sequence reconstructions. At the protein level, empirical …

Comparative sequence analyses, including such fundamental bioinformatics techniques as
similarity searching, sequence alignment and phylogenetic inference, have become a …

The blind use of models of nucleotide substitution in evolutionary analyses is a common
practice in the viral community. Typically, a simple model of evolution like the Kimura two …

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 …

The evolution of HIV-1 protein sequences should be governed by a combination of factors
including nucleotide mutational probabilities, the genetic code, and fitness. The impact of …

A hallmark of the human immunodeficiency virus 1 (HIV-1) is its rapid rate of evolution within
and among its various subtypes. Two complementary hypotheses are suggested to explain …

Natural selection imposes a complex filter on which variants persist in a population resulting
in evolutionary patterns that vary greatly along the genome. Some sites evolve close to …

Abstract Human immunodeficiency virus 1 (HIV-1) is a rapidly evolving virus able to evade
host immunity through rapid adaptation during chronic infection. The HIV-1 group M has …

Our goal is to understand how enzymes adapt to utilize novel substrates. We and others
have shown that directed evolution tends to generate enzyme variants with broadened …