Florent, Isabelle, Porcel, Betina M, Guillaume, Elodie, Da Silva, Corinne, Artiguenave, François, Maréchal, Eric, ...
Abstract Background The Plasmodium falciparum genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for...
Evolution of Tandemly Repeated Sequences through Duplication and Inversion (2009)
Denis Bertr, Mathieu Lajoie, Nadia El-mabrouk, Olivier Gascuel
Abstract. Given a phylogenetic tree T for a family of tandemly repeated genes and their signed order O on the chromosome, we aim to find the minimum number of inversions compatible with an...
Bordewich, Magnus, Gascuel, Olivier, Huber, Katharina, Moulton, Vincent
Many phylogenetic algorithms search the space of possible trees using topological rearrangements and some optimality criterion. FastME is such an approach that uses the {em balanced minimum evolution...
Bordewich, Magnus, Gascuel, Olivier, Huber, Katharina, Moulton, Vincent
Many phylogenetic algorithms search the space of possible trees using topological rearrangements and some optimality criterion. FastME is such an approach that uses the {em balanced minimum evolution...
Florent, Isabelle, Porcel, Betina M, Guillaume, Elodie, Da Silva, Corinne, Artiguenave, François, Maréchal, Eric, ...
Background: The Plasmodium falciparum genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for structural and...
Florent, Isabelle, Porcel, Betina M, Guillaume, Elodie, Da Silva, Corinne, Artiguenave, François, Maréchal, Eric, ...
Background: The Plasmodium falciparum genome (3D7 strain) published in 2002, revealed ~5,400 genes, mostly based on in silico predictions. Experimental data is therefore required for structural and...
Détection de nouveaux domaines protéiques par co-occurence : Application à P. falciparum (2009)
Terrapon, Nicolas, Gascuel, Olivier, Brehelin, Laurent
Hidden Markov Models (HMMs) have proved to be powerful for protein domain identification. However, numerous domains may be missed in highly divergent proteins. This is the case for the proteins of...
Détection de nouveaux domaines protéiques par co-occurence : Application à P. falciparum (2009)
Terrapon, Nicolas, Gascuel, Olivier, Brehelin, Laurent
Hidden Markov Models (HMMs) have proved to be powerful for protein domain identification. However, numerous domains may be missed in highly divergent proteins. This is the case for the proteins of...
Bréhélin, Laurent, Dufayard, Jean-François, Gascuel, Olivier
Abstract Background Of the 5 484 predicted proteins of Plasmodium falciparum , the main causative agent of malaria, about 60% do not have sufficient sequence similarity with proteins in other...
ORIGINAL RESEARCH A Fast and Specific Alignment Method for Minisatellite Maps (2008)
Sèverine Bérard, François Nicolas, Jérôme Buard, Olivier Gascuel, Eric Rivals
Background: Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or...
Stéphane Guindon, Olivier Gascuel
Abstract.—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...
Abstract which the nodes are tests. The leaves, instead of indicating This paper presents a "conceptual regression method". classes, indicate i~tervals of values or single values...
I \.. ~-~i=~:1:~::~ On learning Decision Committees (2008)
Abstract additive fashion, like in MYCIN-type expert systems (Shortliffe [Sh076]). The main idea is to allow the ab-This paper presents decision committees. A sence of an ~ underlying ~rdering. in...
Fast NJ-like algorithms to deal with incomplete distance matrices (2008)
Criscuolo, Alexis, Gascuel, Olivier
Abstract Background Distance-based phylogeny inference methods first estimate evolutionary distances between every pair of taxa, then build a tree from the so-obtained distance matrix. These methods...
Experimental Investigation on the Complexity-Performance Relations (2008)
In Multilayer Perceptrons, Tautvydas Cibas, Patrick Gallinari, Olivier Gascuel, Place Jussieu
This paper describes experimental investigations for exploring the dependence of Neural Networks behavior and capabilities on their complexity. Characteristic behavior patterns are worked out through...
Lirmm Univech Montpefiph, Laurent Bréhélin, Olivier Gascuel, Gilles Caraux
prehfi t a ne w modefi defiy e from lassi al Hidde n Markov Modey (HMMs), tolehT se ue n e of large BooleP ve tors. Our mo de -- Hidden Markov Model with Patterns,orHMMP --di#e rsfrom HMM by the fa t...
Evidence for a Relationship Between Algorithmic Scheme (2008)
Agglomeration and addition are the two main algorithmic schemes for constructing a tree distance from a dissimilarity matrix. The former scheme iteratively agglomerates pairs of leaves to form larger...
PHYML Online - a web server for fast maximum likelihood-based phylogenetic inference (2008)
Stephane Guindon, Franck Lethiec, Patrice Duroux, Olivier Gascuel, Olivier Gascuel
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...
Hidden Markov and Independence Models with Patterns for Sequential BIST (2008)
Laurent Brehelin Olivier, Olivier Gascuel, Gilles Caraux, Patrick Girard, Christian Landrault
We propose a novel BIST technique for non-scan sequential circuits which does not modify the circuit under test. It uses a learning algorithm to build a hardware test sequence generator capable of...
Using Repeated Measurements to Validate Hierarchical Gene Clusters (2008)
Brehelin, Laurent, Gascuel, Olivier, Martin, Olivier
Motivation: Hierarchical clustering is a common approach to study protein and gene expression data. This unsupervised technique is used to find clusters of genes or proteins which are expressed in a...
Using Repeated Measurements to Validate Hierarchical Gene Clusters (2008)
Brehelin, Laurent, Gascuel, Olivier, Martin, Olivier
Motivation: Hierarchical clustering is a common approach to study protein and gene expression data. This unsupervised technique is used to find clusters of genes or proteins which are expressed in a...
Empirical Profile Mixture Models for Phylogenetic Reconstruction (2008)
Le, Quang, Gascuel, Olivier, Lartillot, Nicolas
MOTIVATION: Previous studies have shown that accounting for sitespecific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving...
Phylogeny.fr: robust phylogenetic analysis for the non-specialist (2008)
Dereeper, Alexis, Guignon, Valentin, Blanc, Guillaume, Audic, Stéphane, Buffet, Sylvain, Chevenet, François, ...
Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the...
Empirical Profile Mixture Models for Phylogenetic Reconstruction (2008)
Le, Quang, Gascuel, Olivier, Lartillot, Nicolas
MOTIVATION: Previous studies have shown that accounting for sitespecific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving...
Phylogeny.fr: robust phylogenetic analysis for the non-specialist (2008)
Dereeper, Alexis, Guignon, Valentin, Blanc, Guillaume, Audic, Stéphane, Buffet, Sylvain, Chevenet, François, ...
Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the...
Une approche phylo-HMM pour la recherche de séquences (2008)
Domelevo Entfellner, Jean-Baka, Gascuel, Olivier
We introduce a new type of phylogenetic Hidden Markov Model, combining the strength of usual HMM and the knowledge of the phylogeny of a family of sequences.We use such models to look into the genome...
Une approche phylo-HMM pour la recherche de séquences (2008)
Domelevo Entfellner, Jean-Baka, Gascuel, Olivier
We introduce a new type of phylogenetic Hidden Markov Model, combining the strength of usual HMM and the knowledge of the phylogeny of a family of sequences.We use such models to look into the genome...
Fast NJ-Like Algorithms to Deal with Incomplete Distance Matrices (2008)
Criscuolo, Alexis, Gascuel, Olivier
BACKGROUND: Distance-based phylogeny inference methods first estimate evolutionary distances between every pair of taxa, then build a tree from the so-obtained distance matrix. These methods are fast...
Desper, Richard, Gascuel, Olivier
Synonyms and Index Terms: phylogeny reconstruction, distance methods, performance analysis, robustness, safety radius approach, optimal radius
Bréhélin, Laurent, Dufayard, Jean-François, Gascuel, Olivier
Background: Of the 5,484 predicted proteins of Plasmodium falciparum, the main causative agent of malaria, about 60\% do not have sufficient sequence similarity with proteins in other organisms to...
Bréhélin, Laurent, Dufayard, Jean-François, Gascuel, Olivier
Background: Of the 5,484 predicted proteins of Plasmodium falciparum, the main causative agent of malaria, about 60\% do not have sufficient sequence similarity with proteins in other organisms to...
Desper, Richard, Gascuel, Olivier
Synonyms and Index Terms: phylogeny reconstruction, distance methods, performance analysis, robustness, safety radius approach, optimal radius
Fast NJ-Like Algorithms to Deal with Incomplete Distance Matrices (2008)
Criscuolo, Alexis, Gascuel, Olivier
BACKGROUND: Distance-based phylogeny inference methods first estimate evolutionary distances between every pair of taxa, then build a tree from the so-obtained distance matrix. These methods are fast...
An improved general amino acid replacement matrix (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. They...
An improved general amino acid replacement matrix (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. They...
Phylogenetic Mixture Models for Proteins (2008)
Le, Quang, Lartillot, Nicolas, Gascuel, Olivier
Standard protein substitution models use a single amino-acid replacement rate matrix which summarizes the biological, chemical and physical properties of amino acids. However, site evolution is...
Phylogenetic Mixture Models for Proteins (2008)
Le, Quang, Lartillot, Nicolas, Gascuel, Olivier
Standard protein substitution models use a single amino-acid replacement rate matrix which summarizes the biological, chemical and physical properties of amino acids. However, site evolution is...
Empirical profile mixture models for phylogenetic reconstruction (2008)
Si Quang, Le, Gascuel, Olivier, Lartillot, Nicolas
Motivation: Previous studies have shown that accounting for site-specific amino acid replacement patterns using mixtures of stationary probability profiles offers a promising approach for improving...
An Improved General Amino Acid Replacement Matrix (2008)
Le, Si Quang, Gascuel, Olivier
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. They...
Bmc Bioinformatics, Laurent Bréhélin, Jean-françois Dufayard, Olivier Gascuel
Research article PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data
Experimental investigation on the complexity-performance relations in Multilayer Perceptrons (2007)
Tautvydas Cibas, Patrick Gallinari, Olivier Gascuel, Place Jussieu
This paper describes experimental investigations for exploring the dependence of Neural Networks behavior and capabilities on their complexity. Characteristic behavior patterns are worked out through...
running head: COUNTING DUPLICATION TREES The Combinatorics of Tandem Duplication Trees (2007)
Olivier Gascuel, Michael D. Hendy, Alain Jean-marie, Robert Mclachlan
We develop a recurrence relation that counts the number of Tandem Duplication Trees (either rooted or unrooted) that are consistent with a set of n tandemly repeated sequences generated under the...
In this paper we will present UNJ, an unweighted version of the NJ algorithm (Saitou and Nei 1987; Studier and Keppler 1988). We will demonstrate that UNJ is well suited when the data are of the
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood (2007)
Guindon, Stephane, Gascuel, Olivier
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 new...
Duplication and Inversion History of a Tandemly Repeated Genes Family (2007)
Lajoie, Mathieu, Bertrand, Denis, El-Mabrouk, Nadia, Gascuel, Olivier
Given a phylogenetic tree for a family of tandemly repeated genes and their signed order on the chromosome, we aim to find the minimum number of inversions compatible with an evolutionary history of...
Genomics, biogeography, and the diversification of placental mammals (2007)
E. Wildman, Derek, Uddin, Monica, C. Opazo, Juan, Liu, Guozhen, Lefort, Vincent, Guindon, Stephane, ...
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...
Brehelin, Laurent, Gascuel, Olivier
Most genomes contain large amounts of orphan genes. For example, 60\% of the P.falciparum genes (the main causal agent of Malaria) lack functional annotation. New approaches, commonly referred as...
Duplication and Inversion History of a Tandemly Repeated Genes Family (2007)
Lajoie, Mathieu, Bertrand, Denis, El-Mabrouk, Nadia, Gascuel, Olivier
Given a phylogenetic tree for a family of tandemly repeated genes and their signed order on the chromosome, we aim to find the minimum number of inversions compatible with an evolutionary history of...
Genomics, biogeography, and the diversification of placental mammals (2007)
E. Wildman, Derek, Uddin, Monica, C. Opazo, Juan, Liu, Guozhen, Lefort, Vincent, Guindon, Stephane, ...
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...
Brehelin, Laurent, Gascuel, Olivier
Most genomes contain large amounts of orphan genes. For example, 60\% of the P.falciparum genes (the main causal agent of Malaria) lack functional annotation. New approaches, commonly referred as...
Mirabeau, Olivier, Perlas, Emerald, Severini, Cinzia, Audero, Enrica, Gascuel, Olivier, Possenti, Roberta, ...
Peptide hormones are small, processed, and secreted peptides that signal via membrane receptors and play critical roles in normal and pathological physiology. The search for novel peptide hormones...
Brehelin, Laurent, Gascuel, Olivier
The guilt by association (GBA) principle is used in several supervised and non-supervised methods to functionally annotate uncharacterized genes from transcriptomic data or from other information...
A Fast and Specific Alignment Method for Minisatellite Maps (2006)
Bérard, Sèverine, Nicolas, François, Buard, Jérome, Gascuel, Olivier, Rivals, Eric
Background: Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or...
A Fast and Specific Alignment Method for Minisatellite Maps (2006)
Bérard, Sèverine, Nicolas, François, Buard, Jérome, Gascuel, Olivier, Rivals, Eric
Background: Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or...
Brehelin, Laurent, Gascuel, Olivier
The guilt by association (GBA) principle is used in several supervised and non-supervised methods to functionally annotate uncharacterized genes from transcriptomic data or from other information...
A Fast and Specific Alignment Method for Minisatellite Maps (2006)
Sèverine Bérard, François Nicolas, Jérôme Buard, Olivier Gascuel, Eric Rivals
Background: Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or...
A Fast and Specific Alignment Method for Minisatellite Maps (2006)
Sèverine Bérard, François Nicolas, Jérôme Buard, Olivier Gascuel, Eric Rivals
Background: Variable minisatellites count among the most polymorphic markers of eukaryotic and prokaryotic genomes. This variability can affect gene coding regions, like in the prion protein gene, or...
Neighbor-Joining Revealed (2006)
It is nearly 20 years since the landmark paper (Saitou and Nei 1987) in Molecular Biology and Evolution introducing Neighbor-Joining (NJ). The method has become the most widely used method for...
Neighbor-Joining Revealed (2006)
It is nearly 20 years since the landmark paper (Saitou and Nei, 1987) in MBE introducing Neighbor-Joining (NJ). The method has become the most widely-used method for building phylogenetic trees from...
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative (2006)
Anisimova, Maria, Gascuel, Olivier
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...
SDM: A Fast Distance-Based Approach for (Super)Tree Building in Phylogenomics (2006)
Criscuolo, Alexis, Berry, Vincent, Douzery, Emmanuel J. P., Gascuel, Olivier
Phylogenomic studies aim to build phylogenies from large sets of homologous genes. Such “genome-sized” data require fast methods, because of the typically large numbers of taxa examined. In this...
PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference (2005)
Stéphane Guindon, Franck Lethiec, Patrice Duroux, Olivier Gascuel
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...
Topological rearrangements and local search method for tandem duplication trees (2005)
Denis Bertrand, Olivier Gascuel
The problem of reconstructing the duplication history of a set of tandemly repeated sequences was first introduced by Fitch [4]. Many recent studies deal with this problem, showing the validity of...
A Simple Method to Predict Protein Binding From Aligned Sequences (2005)
Application To Mhc, Elodie Duprat, Marie-paule Lefranc, Olivier Gascuel
Motivation: The MHC superfamily (MhcSF) consists of immune system MHC class I (MHC-I) proteins, along with proteins with a MHC-I-like structure that are involved in a large variety of biological...
Motivation: Maximum likelihood methods have become very popular for constructing phylogenetic trees from sequence data. However, despite noticeable recent progress, with large and difficult data sets...
Sylvie Pinloche, Olivier Gascuel, Jacques Van Helden
Motivation: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p, respectively. The binding sites for these factors share a common core CACGTG. We...
Hordijk, Wim, Gascuel, Olivier
Motivation: Maximum likelihood (ML) methods have become very popular for constructing phylogenetic trees from sequence data. However, despite noticeable recent progress, with large and difficult...
PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference (2005)
Guindon, Stéphane, Lethiec, Franck, Duroux, Patrice, Gascuel, Olivier
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...
Gonze, Didier, Pinloche, Sylvie, Gascuel, Olivier, Van Helden, Jacques
Motivation: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p, respectively. The binding sites for these factors share a common core CACGTG. We...
Gonze, Didier, Pinloche, Sylvie, Gascuel, Olivier, Van Helden, Jacques
Motivation: In yeast, methionine and phosphate metabolism are regulated by the complexes Met4p/Met28p/Cbf1p and Pho4p respectively. The binding sites for these factors share a common core CACGTG. We...
Hordijk, Wim, Gascuel, Olivier
Motivation: Maximum likelihood methods have become very popular for constructing phylogenetic trees from sequence data. However, despite noticeable recent progress, with large and difficult data sets...
Duprat, Elodie, Lefranc, Marie-Paule, Gascuel, Olivier
Motivation: The MHC superfamily (MhcSF) consists of immune system MHC class I (MHC-I) proteins, along with proteins with a MHC-I-like structure that are involved in a large variety of biological...
Desper, Richard, Gascuel, Olivier
Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (R. Desper and O. Gascuel, J. Comp. Biol. 9:687–705, 2002), we introduced...
The Combinatorics of Tandem Duplication Trees (2003)
Gascuel, Olivier, Hendy, M., Jean-Marie, Alain, Mclachlan, R.
N/A
The Combinatorics of Tandem Duplication Trees (2003)
Gascuel, Olivier, Hendy, M., Jean-Marie, Alain, Mclachlan, R.
N/A
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by . . . (2003)
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 new...
Desper, Richard, Gascuel, Olivier
Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (Desper and Gascuel 2002), we introduced a new "balanced" minimum evolution...
Desper, Richard, Gascuel, Olivier
Due to its speed, the distance approach remains the best hope for building phylogenies on very large sets of taxa. Recently (Desper and Gascuel 2002), we introduced a new "balanced" minimum evolution...
The Combinatorics of Tandem Duplication Trees (2003)
Gascuel, Olivier, Hendy, Michael D., Jean-Marie, Alain, McLachlan, Robert
We developed a recurrence relation that counts the number of tandem duplication trees (either rooted or unrooted) that are consistent with a set of n tandemly repeated sequences generated under the...
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood (2003)
Guindon, Stéphane, Gascuel, Olivier
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 new...
Richard Desper, Olivier Gascuel
The Minimum Evolution (ME) approach to phylogeny estimation has been shown to be statistically consistent when it is used in conjunction with ordinary least-squares (OLS) fitting of a metric to a...
Syst. Biol. 52(1):110--118, 2003 (2002)
Doi The Combinatorics, Olivier Gascuel, Michael D. Hendy, Alain Jean-marie, Robert Mclachlan
Wedeveloped a recurrence relation that counts the number of tandem duplication trees (either rooted or unrooted) that are consistent with a set of n tandemly repeated sequences generated under the...
Vol Suppl Pages, Olivier Elemento, Olivier Gascuel
The problem of reconstructing the duplication tree of a set of tandemly repeated sequences which are supposed to have arisen through unequal recombination, was first introduced by Fitch (1977,...
Richard Desper, Olivier Gascuel
This paper investigates the standard ordinary least-squares version [24] and the balanced version [20] of the minimum evolution principle. For the standard version, we provide a greedy construction...
Richard Desper, Olivier Gascuel
The Minimum Evolution (ME) approach to phylogeny estimation has been shown to be statistically consistent when it is used in conjunction with ordinary least-squares (OLS) fitting of a metric to a...
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees (2002)
Elemento, Olivier, Gascuel, Olivier
The problem of reconstructing the duplication tree of a set of tandemly repeated sequences which are supposed to have arisen through unequal recombination, was first introduced by Fitch (1977,...
Reconstructing the Duplication History of Tandemly Repeated Genes (2002)
Elemento, Olivier, Gascuel, Olivier, Lefranc, Marie-Paule
We present a novel approach to deal with the problem of reconstructing the duplication history of tandemly repeated genes that are supposed to have arisen from unequal recombination. We first...
Guindon, Stéphane, Gascuel, Olivier
This paper deals with phylogenetic inference when the variability of substitution rates across sites (VRAS) is modeled by a gamma distribution. We show that underestimating VRAS, which results in...
Ranwez, Vincent, Gascuel, Olivier
We introduce a new approach to estimate the evolutionary distance between two sequences. This approach uses a tree with three leaves: two of them correspond to the studied sequences, whereas the...
Quartet-Based Phylogenetic Inference: Improvements and Limits (2001)
Ranwez, Vincent, Gascuel, Olivier
We analyze the performance of quartet methods in phylogenetic reconstruction. These methods first compute four-taxon trees (4-trees) and then use a combinatorial algorithm to infer a phylogeny that...
Inferring Evolutionary Trees With Strong Combinatorial Evidence (2000)
Vincent Berry, Olivier Gascuel
We consider the problem of inferring the evolutionary tree of a set of n species. We propose a quartet reconstruction method which speci#cally produces trees whose edges have strong combinatorial...
On the Optimization Principle in Phylogenetic Analysis and the Minimum-Evolution Criterion (2000)
This paper discusses the optimization principle in phylogenetic analysis, in the case of distance data. We argue that the use of this principle cannot be called into question, except for computing...
Inferring Evolutionary Trees with Strong Combinatorial Evidence (1997)
Vincent Berry Olivier, Olivier Gascuel, Of Q
We consider the problem of inferring the evolutionary tree of a set of n species. We propose a quartet reconstruction method which specifically produces trees whose edges have strong combinatorial...
Concerning the NJ algorithm and its unweighted version, UNJ (1997)
Olivier Gascuel Gerad, Olivier Gascuel
In this paper we will present UNJ, an unweighted version of the NJ algorithm (Saitou and Nei 1987; Studier and Keppler 1988). We will demonstrate that UNJ is well suited when the data are of the ##...
Berry, Vincent, Gascuel, Olivier
In this study we address the problem of interpreting a bootstrap tree. The main issue is choosing the threshold of clade selection in order to separate reliable clades from unreliable ones, depending...
resubstitution error estimate (1992)
Olivier Gascuel, Gilles Caraux
Distribution-free performance bounds with the
Statistical significance in inductive learning (1992)
Olivier Gascuel, Gilles Caraux
Abstract, Inductive learning systems search for regularities that therefore be applied with some assurance to an example describe environmental observations, These systems often use which does not...
PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference
Guindon, Stéphane, Lethiec, Franck, Duroux, Patrice, Gascuel, Olivier
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...
PHYML Online—a web server for fast maximum likelihood-based phylogenetic inference
Guindon, Stéphane, Lethiec, Franck, Duroux, Patrice, Gascuel, Olivier
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...
Identification of novel peptide hormones in the human proteome by hidden Markov model screening
Mirabeau, Olivier, Perlas, Emerald, Severini, Cinzia, Audero, Enrica, Gascuel, Olivier, Possenti, Roberta, ...
Peptide hormones are small, processed, and secreted peptides that signal via membrane receptors and play critical roles in normal and pathological physiology. The search for novel peptide hormones...
Genomics, biogeography, and the diversification of placental mammals
Wildman, Derek E., Uddin, Monica, Opazo, Juan C., Liu, Guozhen, Lefort, Vincent, Guindon, Stephane, ...
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...
A reduction algorithm for approximating a (nonmetric) dissimilarity by a tree distance
Tree distance, Heuristic algorithm, Least-squares projection, Convex polyhedral cones, Computer simulations,
PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data
Bréhélin, Laurent, Dufayard, Jean-François, Gascuel, Olivier