Knowing phylogenetic relationships among species is fundamental for many studies in
biology. An accurate phylogenetic tree underpins our understanding of the major transitions …

Background Due to the national dynamic zero-COVID strategy in China, there were no
persistent local transmissions of SARS-CoV-2 in Bei**g before December, 2022. However …

Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite
of models. Consequently, users of these software packages are simultaneously forced to …

Large phylogenomics data sets require fast tree inference methods, especially for maximum-
likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find …

In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix,
is commonly accompanied by the assumption of partition models. Under such models each …

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been
viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life …

Time-stamped, trait-annotated phylogenetic trees built from virus genome data are
increasingly used for outbreak investigation and monitoring ongoing epidemics. This …

BEAGLE is a high-performance likelihood-calculation library for phylogenetic inference. The
BEAGLE library defines a simple, but flexible, application programming interface (API), and …

Inference of phylogenetic trees under the maximum likelihood (ML) criterion represents a
routine task in biological data analysis. In this unit we describe how to plan analyses and …

The sizes of the data matrices assembled to resolve branches of the tree of life have
increased dramatically, motivating the development of programs for fast, yet accurate …