Fifty years ago, a Science paper by Atchison et al. reported a newly discovered virus that
would soon become known as adeno-associated virus (AAV) and that would subsequently …

Since its introduction in the human population, SARS-CoV-2 has evolved into multiple
clades, but the events in its intrahost diversification are not well understood. Here, we …

Mutation and recombination drive the evolution of most pathogens by generating the genetic
variants upon which selection operates. Those variants can, for example, confer resistance …

The selection of the best-fitting substitution model of molecular evolution is a traditional step
for phylogenetic inferences, including ancestral sequence reconstruction (ASR). However, a …

The changes occurring in viral quasispecies populations during infection have been
monitored using diversity indices, nucleotide diversity, and several other indices to …

One of the most intriguing puzzles in biology is the degree to which evolution is repeatable.
The repeatability of evolution, or parallel evolution, has been studied in a variety of model …

Since its introduction in the human population, SARS-CoV-2 has evolved into multiple
clades, but the events in its intrahost diversification are not well understood. Here, we …

ABSTRACT RNA viruses replicate as complex mutant spectra termed viral quasispecies.
The frequency of each individual genome in a mutant spectrum depends on its rate of …

Probabilistic phylogenetic tree reconstruction is traditionally performed under a best-fitting
substitution model of molecular evolution previously selected according to diverse statistical …

A self-organizing map (SOM) is an artificial neural network algorithm that can learn from the
training data consisting of objects expressed as vectors and perform non-hierarchical …