Many models of evolution calculate the rate of evolution by multiplying the rate at which new
mutations originate within a population by a probability of fixation. Here we review the …

The phenotypic effect of an allele at one genetic site may depend on alleles at other sites, a
phenomenon known as epistasis. Epistasis can profoundly influence the process of …

Numerous computational methods exist to assess the mode and strength of natural selection
in protein-coding sequences, yet how distinct methods relate to one another remains largely …

Adaptation in protein-coding sequences can be detected from multiple sequence alignments
across species or alternatively by leveraging polymorphism data within a population. Across …

When mutational pressure is weak, the generative process of protein evolution involves
explicit probabilities of mutations of different types coupled to their conditional probabilities …

Motivation: In recent years, there has been an increasing interest in the potential of codon
substitution models for a variety of applications. However, the computational demands of …

We develop a maximum penalized-likelihood (MPL) method to estimate the fitnesses of
amino acids and the distribution of selection coefficients (S= 2 Ns) in protein-coding genes …

Codon substitution models have traditionally attempted to uncover signatures of adaptation
within protein-coding genes by contrasting the rates of synonymous and non-synonymous …

Substitutions between chemically distant amino acids are known to occur less frequently
than those between more similar amino acids. This knowledge, however, is not reflected in …

Phylogeny-based modeling of heterogeneity across the positions of multiple-sequence
alignments has generally been approached from two main perspectives. The first treats site …