Assessing the effect of methodological decisions on the resulting hypotheses is critical in
phylogenetics. Recent studies have focused on evaluating how model selection, orthology …

Several strategies have been proposed to assign substitution models in phylogenomic
datasets, or partitioning. The accuracy of these methods, and most importantly, their impact …

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 …

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

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 …

As phylogenomic datasets have grown in size, researchers have developed new ways to
measure biological variation and to assess statistical support. Larger datasets have many …

Systematic biases such as long branch attraction can mislead commonly relied upon model-
based (ie maximum likelihood and Bayesian) phylogenetic methods when, as is usually the …

Topological conflict or incongruence is widespread in phylogenomic data. Concatenation-
and coalescent-based approaches often result in incongruent topologies, but the causes of …

The availability of phylogenetic data has greatly expanded in recent years. As a result, a
new era in phylogenetic analysis is dawning—one in which the methods we use to analyse …

Molecular phylogenetics relies on accurate identification of orthologous sequences among
the taxa of interest. Most orthology inference programs available for use in phylogenomics …