V. Lefort

Publications
Influence

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, Wim Hordijk, O. Gascuel
Biology, Medicine
Systematic biology
29 March 2010

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 tree… Expand

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Phylogeny.fr: robust phylogenetic analysis for the non-specialist

A. Dereeper, V. Guignon, +9 authors O. Gascuel
Biology, Medicine
Nucleic Acids Res.
19 April 2008

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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213
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SMS: Smart Model Selection in PhyML

V. Lefort, J. Longueville, O. Gascuel
Biology, Medicine
Molecular biology and evolution
11 May 2017

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

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program

V. Lefort, Richard Desper, O. Gascuel
Biology, Computer Science
Molecular biology and evolution
30 June 2015

FastME provides distance algorithms to infer phylogenies, while remaining as fast as Neighbor Joining. Expand

Genomics, biogeography, and the diversification of placental mammals

D. Wildman, M. Uddin, +7 authors M. Goodman
Biology, Medicine
Proceedings of the National Academy of Sciences
4 September 2007

Previous molecular analyses of mammalian evolutionary relationships involving a wide range of placental mammalian taxa have been restricted in size from one to two dozen gene loci and have not… Expand

Characterization of 43 Non-Protein-Coding mRNA Genes in Arabidopsis, Including the MIR162a-Derived Transcripts1[W]

Judith Hirsch, V. Lefort, +5 authors M. Crespi
Biology, Medicine
Plant Physiology
24 February 2006

Messenger RNAs that do not contain a long open reading frame (ORF) or non-protein-coding RNAs (npcRNAs) are an emerging novel class of transcripts. Their functions may involve the RNA molecule itself… Expand

Analyses of Phylogenetics and Evolution

E. Paradis, S. Blomberg, +21 authors D. D. Vienne
Biology
29 November 2015

PhySIC_IST: cleaning source trees to infer more informative supertrees

Céline Scornavacca, V. Berry, V. Lefort, E. Douzery, V. Ranwez
Computer Science, Biology
BMC Bioinformatics
4 October 2008

The paper introduces and tests two new methodologies, PhySIC_IST and STC, that demonstrate the interest in inferring non-plenary supertrees as well as preprocessing the source trees. Expand

NGPhylogeny.fr: new generation phylogenetic services for non-specialists

F. Lemoine, Damien Correia, +4 authors O. Gascuel
Biology, Medicine
Nucleic acids research
27 April 2019

Abstract Phylogeny.fr, created in 2008, has been designed to facilitate the execution of phylogenetic workflows, and is nowadays widely used. However, since its development, user needs have evolved,… Expand

TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

J. Chang, P. D. Tommaso, V. Lefort, O. Gascuel, C. Notredame
Computer Science, Biology
Nucleic Acids Res.
8 April 2015

This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index. Expand

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