Molecular phylogenies are a cornerstone of modern comparative biology and are commonly
employed to investigate a range of biological phenomena, such as diversification rates …

The scale of data sets used to infer phylogenies has grown dramatically in the last decades,
providing researchers with an enormous amount of information with which to draw …

Disagreement or conflict among phylogenetic hypotheses obtained by analysis of large,
genomewide data sets has incited debate over potential benefits, pitfalls, and best practices …

Over the last decade, molecular systematics has undergone a change of paradigm as high-
throughput sequencing now makes it possible to reconstruct evolutionary relationships …

Current phylogenomic methods are still a long way from implementing a realistic genome
evolution model. An ideal approach would require a general joint analysis of genomic …

Background Phylogenomic approaches have great power to reconstruct evolutionary
histories, however they rely on multi-step processes in which each stage has the potential to …

Reconstructing the evolutionary relationships of species is a major goal in biology. Despite
the increasing number of completely sequenced genomes, a large number of phylogenetic …

Purpose One of our central research goals is to identify evolution's greatest innovations. The
space we're searching (ie, the entire tree of life) is vast and remains mostly uncharted …

Motivation: Species tree estimation in the presence of incomplete lineage sorting (ILS) is a
major challenge for phylogenomic analysis. Although many methods have been developed …

Phylogenomics refers to the inference of historical relationships among species using
genome-scale sequence data and to the use of phylogenetic analysis to infer protein …