PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML
versions used a fast algorithm performing nearest neighbor interchanges to improve a …

We present SeaView version 4, a multiplatform program designed to facilitate multiple
alignment and phylogenetic tree building from molecular sequence data through the use of a …

The increase in the number of large data sets and the complexity of current probabilistic
sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. …

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

We revisit statistical tests for branches of evolutionary trees reconstructed upon molecular
data. A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a …

Amino acid replacement matrices are an essential basis of protein phylogenetics. They are
used to compute substitution probabilities along phylogeny branches and thus the likelihood …

We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei.
This new algorithm, BIONJ, follows the same agglomerative scheme as NJ, which consists of …

Abstract Model selection using likelihood-based criteria (eg, AIC) is one of the first steps in
phylogenetic analysis. One must select both a substitution matrix and a model for rates across …

PHYML Online is a web interface to PHYML, a software that implements a fast and accurate
heuristic for estimating maximum likelihood phylogenies from DNA and protein sequences. …

FastME provides distance algorithms to infer phylogenies. FastME is based on balanced
minimum evolution, which is the very principle of Neighbor Joining (NJ). FastME improves over …