Motivation Phylogenies are important for fundamental biological research, but also have
numerous applications in biotechnology, agriculture and medicine. Finding the optimal tree …

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 …

Motivation: Phylogenies are increasingly used in all fields of medical and biological
research. Moreover, because of the next-generation sequencing revolution, datasets used …

The fields of phylogenetic tree and network inference have dramatically advanced in the last
decade, but independently with few attempts to bridge them. Here we provide a framework …

Modern sequencing technology now allows biologists to collect the entirety of molecular
evidence for reconstructing evolutionary trees. We introduce a novel, user-friendly software …

A comprehensive account of both basic and advanced material in phylogeny estimation,
focusing on computational and statistical issues. No background in biology or computer …

Abstract We introduce the Phylogenetic Likelihood Library (PLL), a highly optimized
application programming interface for developing likelihood-based phylogenetic inference …

Characterizing and quantifying genome size variation among organisms and understanding
if genome size evolves as a consequence of adaptive or stochastic processes have been …

Motivation: Due to advances in molecular sequencing and the increasingly rapid collection
of molecular data, the field of phyloinformatics is transforming into a computational science …

We reconstructed a phylogenetic tree of Chinese vascular plants (Tracheophyta) using
sequences of the chloroplast genes atpB, matK, ndhF, and rbcL and mitochondrial matR. We …