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 …

Abstract paml, currently in version 4, is a package of programs for phylogenetic analyses of
DNA and protein sequences using maximum likelihood (ML). The programs may be used to …

There is intense interest in antibody immunity to coronaviruses. However, it is unknown if
coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this …

The magnitude of the COVID-19 pandemic underscores the urgency for a safe and effective
vaccine. Many vaccine candidates focus on the Spike protein, as it is targeted by …

Over the past two decades, comparative sequence analysis using codon-substitution
models has been honed into a powerful and popular approach for detecting signatures of …

Relaxation of selective strength, manifested as a reduction in the efficiency or intensity of
natural selection, can drive evolutionary innovation and presage lineage extinction or loss of …

We present BUSTED, a new approach to identifying gene-wide evidence of episodic
positive selection, where the non-synonymous substitution rate is transiently greater than the …

Since its first release in 2001 as mainly a software package for phylogenetic analysis, data
analysis for molecular biology and evolution (DAMBE) has gained many new functions that …

The imprint of natural selection on protein coding genes is often difficult to identify because
selection is frequently transient or episodic, ie it affects only a subset of lineages. Existing …

Abstract Model-based analyses of natural selection often categorize sites into a relatively
small number of site classes. Forcing each site to belong to one of these classes places …