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A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for… (More)
- Daniel H. Huson, Regula Rupp, Vincent Berry, Philippe Gambette, Christophe Paul
- Bioinformatics
- 2009
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.… (More)
- Philippe Gambette, Vincent Berry, Christophe Paul
- J. Bioinformatics and Computational Biology
- 2012
Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as… (More)
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… (More)
- Philippe Gambette, Leo van Iersel, Michael Peyton Jones, Manuel Lafond, Fabio Pardi, Céline Scornavacca
- PLoS Computational Biology
- 2017
Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement… (More)
- Lionel Spinelli, Philippe Gambette, +6 authors Marie-Christine Brun
- Biosystems
- 2013
BACKGROUND AND SCOPE
Large networks, such as protein interaction networks, are extremely difficult to analyze as a whole. We developed Clust&See, a Cytoscape plugin dedicated to the identification,… (More)
- Christophe Crespelle, Philippe Gambette
- IWOCA
- 2009
In this paper we address the problem of designing O(n) space representations for permutation and interval graphs that provide the neighborhood of any vertex in O(d) time, where d is its degree. To… (More)
The class of 2-interval graphs has been introduced for modelling scheduling and allocation problems, and more recently for specific bioinformatics problems. Some of those applications imply… (More)
- Philippe Gambette, Andreas D. M. Gunawan, Anthony Labarre, Stéphane Vialette, Louxin Zhang
- Discrete Applied Mathematics
- 2017
Abstract A phylogenetic network is a rooted acyclic digraph whose leaves are uniquely labeled with a set of taxa. The tree containment problem asks whether or not a phylogenetic network displays a… (More)
- Christophe Crespelle, Philippe Gambette
- Theor. Comput. Sci.
- 2014
In this paper we show that the contiguity and linearity of cographs on n vertices are both O(logn). Moreover, we show that this bound is tight for contiguity as there exists a family of cographs on n… (More)