The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial
diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles …

Insects comprise over half of all described animal species. Together with the Protura
(coneheads), Collembola (springtails) and Diplura (two-pronged bristletails), insects form …

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 …

The relationships at the root of the animal tree have proven difficult to resolve, with the
current debate focusing on whether sponges (phylum Porifera) or comb jellies (phylum …

A root for the archaeal tree is essential for reconstructing the metabolism and ecology of
early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage …

In phylogenetic inference, we commonly use models of substitution which assume that
sequence evolution is stationary, reversible, and homogeneous (SRH). Although the use of …

Animals make up only a small fraction of the eukaryotic tree of life, yet, from our vantage
point as members of the animal kingdom, the evolution of the bewildering diversity of animal …

Osteoarthritis (OA) has long been viewed as a degenerative disease of cartilage, but
accumulating evidence indicates that inflammation has a critical role in its pathogenesis. In …

Efficient algorithms and programs for the analysis of the ever-growing amount of biological
sequence data are strongly needed in the genomics era. The pace at which new data and …

Recent years have seen a rapid expansion of the model space explored in statistical
phylogenetics, emphasizing the need for new approaches to statistical model representation …