Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for
use in molecular evolution and phylogenetics. APE provides both utility functions for reading …

Phylogenetic analysis aims to establish the true relationships between taxa. Different
analytical methods, however, can reach different conclusions. In order to establish which …

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a
grand challenge. The paucity of homologous character data across disparately related …

DendroPy is a cross-platform library for the Python programming language that provides for
object-oriented reading, writing, simulation and manipulation of phylogenetic data, with an …

Phylogenetic analyses are central to many research areas in biology and typically involve
the identification of homologous sequences, their multiple alignment, the phylogenetic …

Many phylogenetic analyses, particularly morphological studies, use higher taxa (eg,
genera, families) rather than species as terminal taxa. This general approach requires …

RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance
computing) is a sequential and parallel program for inference of large phylogenies with …

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

Phylogenetic trees that include all member lineages are necessary for many questions in
macroevolution, biogeography and conservation. Currently, producing such trees when …

Comparative methods are widely used in ecology and evolution. The most frequently used
comparative methods are based on an explicit evolutionary model. However, recent …