PhyloExplorer: a web server to validate, explore and query phylogenetic trees (2009)
Ranwez, Vincent, Clairon, Nicolas, Delsuc, Frédéric, Pourali, Saeed, Auberval, Nicolas, Diser, Sorel, ...
Abstract Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in...
Linear time 3-approximation for MAST problem (2009)
Berry, Vincent, Paul, Christophe, Guillemot, Sylvain, Nicolas, François
Given a set of leaf-labeled trees with identical leaf sets, the well-known Maximum Agreement Subtree (MAST) problem consists in finding a subtree homeomorphically included in all input trees and...
Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem (2009)
Guillemot, Sylvain, Berry, Vincent
Given a set $L$ of labels and a collection of rooted trees whose leaves are bijectively labelled by some elements of $L$, the Maximum Agreement Supertree problem (SMAST) is as follows: find a tree...
Linear time 3-approximation for MAST problem (2009)
Berry, Vincent, Paul, Christophe, Guillemot, Sylvain, Nicolas, François
Given a set of leaf-labeled trees with identical leaf sets, the well-known Maximum Agreement Subtree (MAST) problem consists in finding a subtree homeomorphically included in all input trees and...
Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem (2009)
Guillemot, Sylvain, Berry, Vincent
Given a set $L$ of labels and a collection of rooted trees whose leaves are bijectively labelled by some elements of $L$, the Maximum Agreement Supertree problem (SMAST) is as follows: find a tree...
From Gene Trees to Species Trees Through a Supertree Approach (2009)
Scornavacca, Celine, Berry, Vincent, Ranwez, Vincent
Gene trees are leaf-labeled trees inferred from molecular se- quences. Due to duplication events arising in genome evolution, gene trees usually have multiple copies of some labels, i.e. species....
From Gene Trees to Species Trees Through a Supertree Approach (2009)
Scornavacca, Celine, Berry, Vincent, Ranwez, Vincent
Gene trees are leaf-labeled trees inferred from molecular se- quences. Due to duplication events arising in genome evolution, gene trees usually have multiple copies of some labels, i.e. species....
Computing Galled Networks from Real Data (2009)
Huson, Daniel, Rupp, Regula, Berry, Vincent, Gambette, Philippe, Paul, Christophe
Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although...
Computing Galled Networks from Real Data (2009)
Huson, Daniel, Rupp, Regula, Berry, Vincent, Gambette, Philippe, Paul, Christophe
Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although...
The Structure of Level-k Phylogenetic Networks (2009)
Gambette, Philippe, Berry, Vincent, Paul, Christophe
Evolution is usually described as a phylogenetic tree, but due to some exchange of genetic material, it can be represented as a phylogenetic network which has an underlying tree structure. The notion...
The Structure of Level-k Phylogenetic Networks (2009)
Gambette, Philippe, Berry, Vincent, Paul, Christophe
Evolution is usually described as a phylogenetic tree, but due to some exchange of genetic material, it can be represented as a phylogenetic network which has an underlying tree structure. The notion...
PhyloExplorer: a web server to validate, explore and query phylogenetic trees. (2009)
Ranwez, Vincent, Clairon, Nicolas, Delsuc, Frédéric, Pourali, Saeed, Auberval, Nicolas, Diser, Sorel, ...
BACKGROUND: Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or...
PhyloExplorer: a web server to validate, explore and query phylogenetic trees. (2009)
Ranwez, Vincent, Clairon, Nicolas, Delsuc, Frédéric, Pourali, Saeed, Auberval, Nicolas, Diser, Sorel, ...
BACKGROUND: Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or...
PhyloExplorer: a web server to validate, explore and query phylogenetic trees (2009)
Ranwez, Vincent, Clairon, Nicolas, Delsuc, Frédéric, Pourali, Saeed, Auberval, Nicolas, Diser, Sorel, ...
Background: Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or...
PhyloExplorer: a web server to validate, explore and query phylogenetic trees (2009)
Ranwez, Vincent, Clairon, Nicolas, Delsuc, Frédéric, Pourali, Saeed, Auberval, Nicolas, Diser, Sorel, ...
Background: Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or...
Computing Galled Networks from Real Data (2009)
Huson, Daniel, Rupp, Regula, Berry, Vincent, Gambette, Philippe, Paul, Christophe
Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although...
Computing Galled Networks from Real Data (2009)
Huson, Daniel, Rupp, Regula, Berry, Vincent, Gambette, Philippe, Paul, Christophe
Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area. Although...
Computing galled networks from real data (2009)
Huson, Daniel H., Rupp, Regula, Berry, Vincent, Gambette, Philippe, Paul, Christophe
Motivation: Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area....
PhySIC_IST: cleaning source trees to infer more informative supertrees (2008)
Scornavacca, Celine, Berry, Vincent, Lefort, Vincent, Douzery, Emmanuel JP, Ranwez, Vincent
Abstract Background Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological...
Emmanuelle Jousselin, Simon Van Noort, Vincent Berry, Jean-Yves Rasplus, Nina Rønsted, Christoff J. Erasmus, ...
The study of chalcid wasps that live within syconia of fig trees (Moraceae, Ficus), provides a unique opportunity to investigate the evolution of specialized communities of insects. By conducting...
V.: Fixed-parameter tractability of the maximum agreement supertree problem (2008)
Sylvain Guillemot, Vincent Berry
Abstract. Given a ground set L of labels and a collection of trees whose leaves are bijectively labelled by some elements of L, the Maximum Agreement Supertree problem (SMAST) is the following: find...
Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem Draft article (2008)
Sylvain Guillemot, Vincent Berry
Abstract. Given a ground set L of labels and a collection of trees whose leaves are bijectively labelled by some elements of L, the Maximum Agreement Supertree problem (SMAST) is the following: find...
On the approximability of the Maximum Agreement SubTree and Maximum Compatible Tree problems (2008)
Guillemot, Sylvain, Nicolas, Francois, Berry, Vincent, Paul, Christophe
This paper has been withdrawn by the corresponding author because the newest version is now published in Discrete Applied Mathematics.
Vincent Ranwez, Vincent Berry, Alexis Criscuolo, Pierre-henri Fabre, Sylvain Guillemot, Celine Scornavacca, ...
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Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem ⋆ (2008)
Sylvain Guillemot, Vincent Berry
Abstract. Given a ground set L of labels and a collection of trees whose leaves are bijectively labelled by some elements of L, the Maximum Agreement Supertree problem (SMAST) is the following: find...
On the Approximation of Computing of (2008)
Evolutionary Trees Research, Vincent Berry, Sylvain Guillemot, François Nicolas, Christophe Paul, Département Informatique
Given a set of leaf-labelled trees with identical leaf sets, the well-known MAST problem consists of finding a subtree homeomorphically included in all input trees and with the largest number of...
From constrained to Unconstrained Maximum Agreement Subtree (2008)
Berry, Vincent, Peng, Zeshan, Ting, H.F.
We propose and study the Maximum Constrained Agreement Sub- tree (MCAST) problem, which is a variant of the classical Maximum Agreement Subtree (MAST) problem. Our problem allows users to ap- ply...
PhySIC IST : cleaning source trees to infer more informative supertrees (2008)
Scornavacca, Celine, Berry, Vincent, Lefort, Alain, Douzery, Emmanuel, Ranwez, Vincent
Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene...
From constrained to Unconstrained Maximum Agreement Subtree (2008)
Berry, Vincent, Peng, Zeshan, Ting, H.F.
We propose and study the Maximum Constrained Agreement Sub- tree (MCAST) problem, which is a variant of the classical Maximum Agreement Subtree (MAST) problem. Our problem allows users to ap- ply...
PhySIC IST : cleaning source trees to infer more informative supertrees (2008)
Scornavacca, Celine, Berry, Vincent, Lefort, Alain, Douzery, Emmanuel, Ranwez, Vincent
Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch attraction, lateral gene transfers, gene duplication/loss or deep gene...
On building and comparing trees Application to supertrees in phylogenetics (2008)
The research work presented in this manuscript is of algorithmic kind: it is mainly composed of polynomial, fixed parameter and approximation algorithms, while hardness results are also mentioned....
On building and comparing trees Application to supertrees in phylogenetics (2008)
The research work presented in this manuscript is of algorithmic kind: it is mainly composed of polynomial, fixed parameter and approximation algorithms, while hardness results are also mentioned....
On building and comparing trees Application to supertrees in phylogenetics (2008)
The research work presented in this manuscript is of algorithmic kind: it is mainly composed of polynomial, fixed parameter and approximation algorithms, while hardness results are also mentioned....
On building and comparing trees Application to supertrees in phylogenetics (2008)
The research work presented in this manuscript is of algorithmic kind: it is mainly composed of polynomial, fixed parameter and approximation algorithms, while hardness results are also mentioned....
From Constrained to Unconstrained Maximum Agreement Subtree in Linear Time (2007)
Berry, Vincent, Peng, Z.S., Ting, H.F.
We propose and study the Maximum Constrained Agreement Subtree (MCAST) problem, which is a variant of the classical Maximum Agreement Subtree (MAST) problem. Our problem allows users to apply their...
From Constrained to Unconstrained Maximum Agreement Subtree in Linear Time (2007)
Berry, Vincent, Peng, Z.S., Ting, H.F.
We propose and study the Maximum Constrained Agreement Subtree (MCAST) problem, which is a variant of the classical Maximum Agreement Subtree (MAST) problem. Our problem allows users to apply their...
An improved polynomial time algorithm for computing the refined Buneman tree (2007)
We consider the problem of inferring a tree with positive weight edges on a set X from a dissimilarity measure on X. This problem, most commonly met in the classification and numerical taxonomy...
Fixed-parameter Tractability of the Maximum Agreement Supertree Problem (2007)
Guillemot, Sylvain, Berry, Vincent
Given a ground set $L$ of labels and a collection of trees whose leaves are bijectively labelled by some elements of $L$, the Maximum Agreement Supertree problem (\pSMAST) is the following: find a...
Fixed-parameter Tractability of the Maximum Agreement Supertree Problem (2007)
Guillemot, Sylvain, Berry, Vincent
Given a ground set $L$ of labels and a collection of trees whose leaves are bijectively labelled by some elements of $L$, the Maximum Agreement Supertree problem (\pSMAST) is the following: find a...
Finding a Largest Subset of Rooted Triples Identifying a Tree is an NP-hard task (2007)
Guillemot, Sylvain, Berry, Vincent
Supertree methods are used to build comprehensive phylogenies from source trees with overlapping sets of leaves. Ranwez et al (2007) recently proposed a polynomial-time method outputting supertrees...
Maximum Agreement and Compatible Supertrees (2007)
Berry, Vincent, Nicolas, François
Given a set of leaf-labelled trees with identical leaf sets, the MAST problem, respectively MCT problem, consists of finding a largest subset of leaves such that all input trees restricted to these...
PhySIC: A Veto Supertree Method with Desirable Properties (2007)
Ranwez, Vincent, Berry, Vincent, Criscuolo, Alexis, Fabre, Pierre-Henri, Guillemot, Sylvain, Scornavacca, Celine, ...
This paper focuses on veto supertree methods, i.e., methods that aim at producing a conservative synthesis of the relationships agreed upon by all source trees. We propose desirable properties that a...
PhySIC: A Veto Supertree Method with Desirable Properties (2007)
Ranwez, Vincent, Berry, Vincent, Criscuolo, Alexis, Fabre, Pierre-Henri, Guillemot, Sylvain, Scornavacca, Celine, ...
This paper focuses on veto supertree methods, i.e., methods that aim at producing a conservative synthesis of the relationships agreed upon by all source trees. We propose desirable properties that a...
Fixed-parameter Tractability of the Maximum Agreement Supertree Problem (2007)
Guillemot, Sylvain, Berry, Vincent
Given a ground set $L$ of labels and a collection of trees whose leaves are bijectively labelled by some elements of $L$, the Maximum Agreement Supertree problem (\pSMAST) is the following: find a...
Maximum Agreement and Compatible Supertrees (2007)
Berry, Vincent, Nicolas, François
Given a set of leaf-labelled trees with identical leaf sets, the MAST problem, respectively MCT problem, consists of finding a largest subset of leaves such that all input trees restricted to these...
Finding a Largest Subset of Rooted Triples Identifying a Tree is an NP-hard task (2007)
Guillemot, Sylvain, Berry, Vincent
Supertree methods are used to build comprehensive phylogenies from source trees with overlapping sets of leaves. Ranwez et al (2007) recently proposed a polynomial-time method outputting supertrees...
Finding a largest subset of rooted triples identifying a tree is an NP-hard task (2007)
Sylvain Guillemot, Vincent Berry
Supertree methods are used to build comprehensive phylogenies from source trees with overlapping sets of leaves. Ranwez et al. (2007) recently proposed a polynomial-time method outputting supertrees...
PhySIC: A Veto Supertree Method with Desirable Properties (2007)
Ranwez, Vincent, Berry, Vincent, Criscuolo, Alexis, Fabre, Pierre-Henri, Guillemot, Sylvain, Scornavacca, Celine, ...
This paper focuses on veto supertree methods; i.e., methods that aim at producing a conservative synthesis of the relationships agreed upon by all source trees. We propose desirable properties that a...
Multipolar Consensus for Phylogenetic Trees (2006)
Bonnard, Cécile, Berry, Vincent, Lartillot, Nicolas
Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of...
Berry, Vincent, Nicolas, François
Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively maximum compatible tree problem (MCT), consists of finding a largest subset of taxa...
Votez veto pour l'Arbre de la Vie (2006)
Berry, Vincent, Ranwez, Vincent, Fabre, Pierre-Henri, Douzery, Emmanuel
Phylogenetic methods are used to infer the evolutionary history of species. In the Tree of Life framework, heterogeneous character data and very large species sets are considered. Supertree methods...
Fast Computation of Supertrees for Compatible Phylogenies with Nested Taxa (2006)
Berry, Vincent, Semple, Charles
Typically, supertree methods combine a collection of source trees in which just the leaves are labelled by taxa. In such methods the resulting supertree is also leaf-labelled. An underlying...
Berry, Vincent, Nicolas, François
Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively maximum compatible tree problem (MCT), consists of finding a largest subset of taxa...
Votez veto pour l'Arbre de la Vie (2006)
Berry, Vincent, Ranwez, Vincent, Fabre, Pierre-Henri, Douzery, Emmanuel
Phylogenetic methods are used to infer the evolutionary history of species. In the Tree of Life framework, heterogeneous character data and very large species sets are considered. Supertree methods...
Fast Computation of Supertrees for Compatible Phylogenies with Nested Taxa (2006)
Berry, Vincent, Semple, Charles
Typically, supertree methods combine a collection of source trees in which just the leaves are labelled by taxa. In such methods the resulting supertree is also leaf-labelled. An underlying...
Multipolar Consensus for Phylogenetic Trees (2006)
Bonnard, Cécile, Berry, Vincent, Lartillot, Nicolas
Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of...
Improved Parameterized Complexity of the (2006)
Maximum Agreement Subtree, Vincent Berry, François Nicolas
Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively maximum compatible tree problem (MCT), consists of finding a largest subset of taxa...
Improved Parameterized Complexity of the (2006)
Maximum Agreement Subtree, Vincent Berry, François Nicolas
Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively maximum compatible tree problem (MCT), consists of finding a largest subset of taxa...
Fast Computation of Supertrees for Compatible (2006)
Phylogenies With Nested, Vincent Berry, Charles Semple
Typically, supertree methods combine a collection of source trees in which just the leaves are labelled by taxa. In such methods the resulting supertree is also leaflabelled.
Improved Parameterized Complexity of the (2006)
Maximum Agreement Subtree, Vincent Berry, François Nicolas
Given a set of evolutionary trees on a same set of taxa, the maximum agreement subtree problem (MAST), respectively maximum compatible tree problem (MCT), consists of finding a largest subset of taxa...
Fast Computation of Supertrees for Compatible Phylogenies with (2006)
Nested Taxa Vincent, Vincent Berry, Charles Semple
Typically, supertree methods combine a collection of source trees in which just the leaves are labelled by taxa. In such methods the resulting supertree is also leaf-labelled. An underlying...
Fast Computation of Supertrees for Compatible Phylogenies with Nested Taxa (2006)
Berry, Vincent, Semple, Charles
Typically, supertree methods combine a collection of source trees in which just the leaves are labeled by taxa. In such methods the resulting supertree is also leaf labeled. An underlying assumption...
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...
Multipolar Consensus for Phylogenetic Trees (2006)
Bonnard, Cécile, Berry, Vincent, Lartillot, Nicolas
Collections of phylogenetic trees are usually summarized using consensus methods. These methods build a single tree, supposed to be representative of the collection. However, in the case of...
On the approximation of computing evolutionary trees (2005)
Vincent Berry, Sylvain Guillemot, François Nicolas, Christophe Paul
Abstract. Given a set of leaf-labelled trees with identical leaf sets, the well-known MAST problem consists of finding a subtree homeomorphically included in all input trees and with the largest...
Maximum Agreement and Compatible Supertrees RR-LIRMM 04045 (2004)
Vincent Berry And, Vincent Berry, François Nicolas
Given a collection of trees on leaves with identical leaf set, the MAST, resp. MCT, problem consists in finding a largest subset of the leaves such that all input trees restricted to this set are...
Maximum Agreement and Compatible Supertrees (2004)
Vincent Berry, François Nicolas
Given a collection of trees on n leaves with identical leaf set, the MAST, resp. MCT, problem consists in finding a largest subset of the leaves such that all input trees restricted to this set are...
A practical algorithm for recovering the best supported edges of an evolutionary tree (2000)
Vincent Berry, David Bryant, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham, ...
It is now routine for biologists to conduct evolutionary analyses of large DNA and protein sequence datasets. A computational bottleneck in these analyses is the recovery of the topology of the...
Vincent Berry, David Bryant, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham, ...
) Vincent Berry David Bryant y Tao Jiang z Paul Kearney x Ming Li -- Todd Wareham k Haoyong Zhang Abstract It is now routine for biologists to conduct evolutionary analyses of large DNA and protein...
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...
Quartet Cleaning: Improved Algorithms and Simulations (1999)
Vincent Berry, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham
A critical step in all quartet methods for constructing evolutionary trees is the inference of the topology for each set of four species (i.e. quartet). It is a well-known fact that all quartet...
Quartet Cleaning: Improved Algorithms and Simulations (1999)
Vincent Berry, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham, Département De Mathématiques, ...
A critical step in all quartet methods for constructing evolutionary trees is the inference of the topology for each set of four sequences (i.e. quartet). It is a well--known fact that all quartet...
An improved polynomial time algorithm for computing the refined Buneman tree (1998)
We consider the problem of inferring a tree with positive weight edges on a set X from a dissimilarity measure on X . This problem arises in classification and more precisely in evolutionary biology,...
Inferring Evolutionary Trees with Strong Combinatorial Evidence (1997)
Vincent Berry, Olivier Gascue, 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...
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...
PhySIC_IST: cleaning source trees to infer more informative supertrees
Scornavacca, Celine, Berry, Vincent, Lefort, Vincent, Douzery, Emmanuel JP, Ranwez, Vincent
PhyloExplorer: a web server to validate, explore and query phylogenetic trees
Ranwez, Vincent, Clairon, Nicolas, Delsuc, Frédéric, Pourali, Saeed, Auberval, Nicolas, Diser, Sorel, ...
Computing galled networks from real data
Huson, Daniel H., Rupp, Regula, Berry, Vincent, Gambette, Philippe, Paul, Christophe
Motivation: Developing methods for computing phylogenetic networks from biological data is an important problem posed by molecular evolution and much work is currently being undertaken in this area....