Recent advances in AI-based protein structure modeling have yielded remarkable progress
in predicting protein structures. Since structures are constrained by their biological function …

Motivation Evolutionary inference depends crucially on the quality of multiple sequence
alignments (MSA), which is problematic for distantly related proteins. Since protein structure …

The ancestral sequence reconstruction (ASR) is a molecular evolution technique that
provides applications to a variety of fields such as biotechnology and biomedicine. To infer …

Motivation Rooted species trees are a basic model with multiple applications throughout
biology, including understanding adaptation, biodiversity, phylogeography and co-evolution …

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

Genetic recombination is a common evolutionary mechanism that produces molecular
diversity. However, its consequences on protein folding stability have not attracted the same …

Motivation The selection among substitution models of molecular evolution is fundamental
for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses …

The evolution of structural proteins is generally constrained by the folding stability. However,
little is known about the particular capacity of viral proteins to accommodate mutations that …

I present here an in-depth, although non-exhaustive, review of two topics in molecular
dating. Clock models, which describe the evolution of the rate of evolution, are considered …

Motivation The evolutionary processes of mutation and recombination, upon which selection
operates, are fundamental to understand the observed molecular diversity. Unlike …