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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
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.
Partitionfinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses.
Two new objective methods for the combined selection of best-fit partitioning schemes and nucleotide substitution models are described and implemented in an open-source program, PartitionFinder, which it is hoped will encourage the objective selection of partitions and thus lead to improvements in phylogenetic analyses.
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.
A Simple, Fast, and Accurate Method to Estimate Large Phylogenies by Maximum Likelihood
- S. Guindon
- Computer Science
A new approach, based on the maximum- likelihood principle, which adjusts tree topology and branch lengths simultaneously and reduces the reduction of computing timeisdramatic in comparison with othermaximum-likelihood packages, while the likelihoodmaximizationabilitytendstobe higher.
Phylogeny.fr: robust phylogenetic analysis for the non-specialist
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.
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…
Estimating maximum likelihood phylogenies with PhyML.
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.
Modeling the site-specific variation of selection patterns along lineages.
- S. Guindon, A. Rodrigo, K. Dyer, J. Huelsenbeck
- BiologyProceedings of the National Academy of Sciences…
- 31 August 2004
An approach that allows the site-specific selection process to vary along lineages of a phylogenetic tree and provides a significantly better fit to the data than one that does not take into account switches between selection patterns in the phylogeny at individual sites is described.
Genomics, biogeography, and the diversification of placental mammals
- D. Wildman, M. Uddin, M. Goodman
- BiologyProceedings of the National Academy of Sciences
- 4 September 2007
Crown placental mammalian diversification appears to be largely the result of ancient plate tectonic events that allowed time for convergent phenotypes to evolve in the descendant clades.