The CODEML program in the PAML package has been widely used to analyze protein-
coding gene sequences to estimate the synonymous and nonsynonymous rates (d S and d …

Over the last decade, a rich variety of massively parallel assays have revolutionized our
understanding of how biological sequences encode quantitative molecular phenotypes …

All modern approaches to molecular phylogenetics require a quantitative model for how
genes evolve. Unfortunately, existing evolutionary models do not realistically represent the …

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 …

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 …

We introduce Pyvolve, a flexible Python module for simulating genetic data along a
phylogeny using continuous-time Markov models of sequence evolution. Easily incorporated …

The evolution of protein-coding genes is usually driven by selective processes, which favor
some evolutionary trajectories over others, optimizing the subsequent protein stability and …

Abstract In Gaussian Process Regression (GPR), hyperparameters are often estimated by
maximizing the marginal likelihood function. However, this data-dominant hyperparameter …

A major current molecular evolution challenge is to link comparative genomic patterns to
species' biology and ecology. Breeding systems are pivotal because they affect many …

Background Sites of positive selection are identified by comparing observed evolutionary
patterns to those expected under a null model for evolution in the absence of such selection …