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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
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. We describe a newExpand
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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
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 reasonable starting treeExpand
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SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
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 graphical userExpand
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Phylogeny.fr: robust phylogenetic analysis for the non-specialist
TLDR
Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, phylogenetic reconstruction and the graphical representation of the inferred tree. Expand
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An improved general amino acid replacement matrix.
  • S. Le, O. Gascuel
  • Medicine, Biology
  • Molecular biology and evolution
  • 1 July 2008
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 of the data. TheyExpand
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BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
  • O. Gascuel
  • Biology, Computer Science
  • Molecular biology and evolution
  • 1 April 1997
TLDR
We propose an improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei. Expand
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PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference
TLDR
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. Expand
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Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.
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 aExpand
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SMS: Smart Model Selection in PhyML
Abstract Model selection using likelihood-based criteria (e.g., AIC) is one of the first steps in phylogenetic analysis. One must select both a substitution matrix and a model for rates across sites.Expand
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Estimating maximum likelihood phylogenies with PhyML.
Our understanding of the origins, the functions and/or the structures of biological sequences strongly depends on our ability to decipher the mechanisms of molecular evolution. These complexExpand
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