It has long been recognized that certain sites within a protein, such as sites in the protein
core or catalytic residues in enzymes, are evolutionarily more conserved than other sites …

Phylogenomics refers to the inference of historical relationships among species using
genome-scale sequence data and to the use of phylogenetic analysis to infer protein …

Abstract Three lineages (BA. 1, BA. 2 and BA. 3) of the severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) Omicron variant of concern predominantly drove South Africa's …

Continued uncontrolled transmission of SARS-CoV-2 in many parts of the world is creating
conditions for substantial evolutionary changes to the virus,. Here we describe a newly …

Continued uncontrolled transmission of the severe acute respiratory syndrome-related
coronavirus 2 (SARS-CoV-2) in many parts of the world is creating the conditions for …

Human respiratory syncytial virus (RSV) is an important cause of acute respiratory infection
with the most severe disease in the young and elderly. Non-pharmaceutical interventions …

Abstract HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source
package for fitting a broad range of evolutionary models to multiple sequence alignments …

Abstract Knowledge of the fitness effects of mutations to SARS-CoV-2 can inform
assessment of new variants, design of therapeutics resistant to escape, and understanding …

Virus host shifts are generally associated with novel adaptations to exploit the cells of the
new host species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus …

Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of
modern comparative sequence analysis. Advances in sequence generation and increased …