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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
- S. Guindon, O. Gascuel
- Computer ScienceSystematic Biology
- 1 October 2003
This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.
- S. Guindon, Jean-François Dufayard, V. Lefort, M. Anisimova, W. Hordijk, O. Gascuel
- Computer ScienceSystematic Biology
- 29 March 2010
A new algorithm to search the tree space with user-defined intensity using subtree pruning and regrafting topological moves and a new test to assess the support of the data for internal branches of a phylogeny are introduced.
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building.
- M. Gouy, S. Guindon, O. Gascuel
- Biology, Computer ScienceMolecular biology and evolution
- 1 February 2010
SeaView version 4 combines all the functions of the widely used programs SeaView and Phylo_win, and expands them by adding network access to sequence databases, alignment with arbitrary algorithm, maximum-likelihood tree building with PhyML, and display, printing, and copy-to-clipboard of rooted or unrooted, binary or multifurcating phylogenetic trees.
Phylogeny.fr: robust phylogenetic analysis for the non-specialist
- A. Dereeper, V. Guignon, O. Gascuel
- BiologyNucleic Acids Res.
- 19 April 2008
The Phylogeny.fr platform transparently chains programs to automatically perform phylogenetic analyses and can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses.
An improved general amino acid replacement matrix.
- S. Le, O. Gascuel
- BiologyMolecular biology and evolution
- 1 July 2008
This method further refine this method by incorporating the variability of evolutionary rates across sites in the matrix estimation and using a much larger and diverse database than BRKALN, which was used to estimate WAG.
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data.
- O. Gascuel
- Computer ScienceMolecular biology and evolution
- 1 April 1997
An improved version of the neighbor-joining (NJ) algorithm of Saitou and Nei, BIONJ, follows the same agglomerative scheme as NJ, which consists of iteratively picking a pair of taxa, creating a new mode which represents the cluster of these taxa and reducing the distance matrix by replacing both taxa by this node.
PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference
- S. Guindon, Franck Lethiec, P. Duroux, O. Gascuel
- Biology, Computer ScienceNucleic Acids Res.
- 27 June 2005
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. This tool provides the…
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative.
- M. Anisimova, O. Gascuel
- MathematicsSystematic Biology
- 1 August 2006
A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as a competitive alternative to nonparametric bootstrap and Bayesian estimation of branch support and is shown to be accurate, powerful, and robust to certain violations of model assumptions.
SMS: Smart Model Selection in PhyML
- V. Lefort, Jean-Emmanuel Longueville, O. Gascuel
- BiologyMolecular biology and evolution
- 11 May 2017
The software, “Smart Model Selection” (SMS), is implemented in the PhyML environment and available using two interfaces: command-line (to be integrated in pipelines) and a web server (http://www.atgc-montpellier.fr/phyml-sms/).
Estimating maximum likelihood phylogenies with PhyML.
- S. Guindon, F. Delsuc, Jean-François Dufayard, O. Gascuel
- BiologyMethods in molecular biology
- 2009
This chapter focuses on phylogenetic tree estimation under the maximum likelihood (ML) principle, a software that implements recent ML phylogenetic methods and algorithms and illustrates the strengths and pitfalls of this program through the analysis of a real data set.
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