Summary Butterflies (Papilionoidea), with over 18,000 described species [1], have
captivated naturalists and scientists for centuries. They play a central role in the study of …

What are the models used in phylogenetic analysis and what exactly is involved in Bayesian
evolutionary analysis using Markov chain Monte Carlo (MCMC) methods? How can you …

Despite recent advances achieved by application of high-performance computing methods
and novel algorithmic techniques to maximum likelihood (ML)-based inference programs …

Trees are a canonical structure for representing evolutionary histories. Many popular criteria
used to infer optimal trees are computationally hard, and the number of possible tree shapes …

Motivation: Bayesian analysis through programs like BEAST (Drummond and Rumbaut,)
and MrBayes (Huelsenbeck et al.,) provides a powerful method for reconstruction of …

Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on
phylogenetic trees that is based on reconstructing many trees from minor variations of the …

Background Analyses of biomolecules for biodiversity, phylogeny or structure/function
studies often use graphical tree representations. Many powerful tree editors are now …

Much progress has been achieved in disentangling evolutionary relationships among
species in the tree of life, but some taxonomic groups remain difficult to resolve despite …

Software for visualizing sequence alignments and trees are essential tools for life scientists.
In this review, we describe the major features and capabilities of a selection of stand-alone …

Production of massive DNA sequence data sets is transforming phylogenetic inference, but
best practices for analyzing such data sets are not well established. One uncertainty is …