Over the past three decades, the Molecular Evolutionary Genetics Analysis (MEGA) software has evolved into a powerful tool with an ever-expanding suite of functionalities. Yet, despite its user-friendly design and widespread adoption by researchers a...
Natural selection leaves detectable patterns of altered spatial diversity within genomes, and identifying affected regions is crucial for understanding species evolution. Recently, machine learning approaches applied to raw population genomic data ha...
Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of sequences descending from a common ancestor. The high computational cost of state-of-the-art maximum likelihood and Bayesian inference methods limits their us...
Phylodynamics is central to understanding infectious disease dynamics through the integration of genomic and epidemiological data. Despite advancements, including the application of deep learning to overcome computational limitations, significant cha...
As population genetic data increase in size, new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient but are not interchangeable with exis...
Inferring past demographic history of natural populations from genomic data is of central concern in many studies across research fields. Previously, our group had developed dadi, a widely used demographic history inference method based on the allele...
MOTIVATION: Simulating multiple sequence alignments (MSAs) using probabilistic models of sequence evolution plays an important role in the evaluation of phylogenetic inference tools and is crucial to the development of novel learning-based approaches...
Inferences of adaptive events are important for learning about traits, such as human digestion of lactose after infancy and the rapid spread of viral variants. Early efforts toward identifying footprints of natural selection from genomic data involve...
Accurate inference of the time to the most recent common ancestor (TMRCA) between pairs of individuals and of the age of genomic variants is key in several population genetic analyses. We developed a likelihood-free approach, called CoalNN, which use...
The recent development of artificial intelligence provides us with new and powerful tools for studying the mysterious relationship between organism evolution and protein evolution. In this work, based on the AlphaFold Protein Structure Database (Alph...