20 citations · 63 across the 23 of their papers we have counts for
25 papers
Average-Tree Phylogenetic Diversity Parameterized by Scanwidth and Invisibility
Leo van Iersel, Mark Jones, Jannik Schestag +2
We investigate parameterized algorithms for computing the average-tree phylogenetic diversity (APD) in rooted phylogenetic networks, studying the problem under different structural…
LvD: A New Algorithm for Computing the Likelihood of a Phylogeny
David Bryant, Celine Scornavacca, David Swofford
There are few, if any, algorithms in statistical phylogenetics which are used more heavily than Felsenstein's 1973 pruning method for computing the likelihood of a tree. We present…
Phylogenetic Network Diversity Parameterized by Reticulation Number and Beyond
Leo van Iersel, Mark Jones, Jannik Schestag +2
Network Phylogenetic Diversity (Network-PD) is a measure for the diversity of a set of species based on a rooted phylogenetic network (with branch lengths and inheritance probabili…
Revisiting Shao and Sokal's index of phylogenetic balance
François Bienvenu, Gabriel Cardona, Celine Scornavacca
Measures of phylogenetic balance, such as the Colless and Sackin indices, play an important role in phylogenetics. Unfortunately, these indices are specifically designed for phylog…
Computing the probability of gene trees concordant with the species tree in the multispecies coalescent
Jakub Truszkowski, Celine Scornavacca, Fabio Pardi
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance…
Cutting an alignment with Ockham's razor
Mark Jones, Philippe Gambette, Leo van Iersel +4
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task i…
Generation of Tree-Child phylogenetic networks
Gabriel Cardona, Joan Carles Pons, Celine Scornavacca
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have bee…
An time Algorithm for computing the Path-length Distance between Trees
David Bryant, Celine Scornavacca
Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a pa…
Reconciling Multiple Genes Trees via Segmental Duplications and Losses
Riccardo Dondi, Manuel Lafond, Celine Scornavacca
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. H…
Exploring the tiers of rooted phylogenetic network space using tail moves
Remie Janssen, Mark Jones, Péter L. Erdős +2
Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rNNI (rooted Nearest Neighbour Interchange) and rSPR (rooted Subtree Prune and…
Finding the most parsimonious or likely tree in a network with respect to an alignment
Steven Kelk, Fabio Pardi, Celine Scornavacca +1
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network const…
Constructing a Consensus Phylogeny from a Leaf-Removal Distance
Cedric Chauve, Mark Jones, Manuel Lafond +2
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possi…
On the Weighted Quartet Consensus problem
Manuel Lafond, Céline Scornavacca
In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of con…
Do branch lengths help to locate a tree in a phylogenetic network?
Philippe Gambette, Leo van Iersel, Steven Kelk +2
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybr…
Efficient FPT algorithms for (strict) compatibility of unrooted phylogenetic trees
Julien Baste, Christophe Paul, Ignasi Sau +1
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species ; these relationships are often depicted via a phylogenetic tree -- a tre…
Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets
Katharina Huber, Leo van Iersel, Vincent Moulton +2
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network…
Exact reconciliation of undated trees
Leo van Iersel, Celine Scornavacca, Steven Kelk
Reconciliation methods aim at recovering macro evolutionary events and at localizing them in the species history, by observing discrepancies between gene family trees and species t…
Kernelizations for the hybridization number problem on multiple nonbinary trees
Leo van Iersel, Steven Kelk, Celine Scornavacca
Given a finite set , a collection of rooted phylogenetic trees on and an integer , the Hybridization Number problem asks if there exists a phylogenetic netw…
On Computing the Maximum Parsimony Score of a Phylogenetic Network
Mareike Fischer, Leo van Iersel, Steven Kelk +1
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization e…
Towards the fixed parameter tractability of constructing minimal phylogenetic networks from arbitrary sets of nonbinary trees
Steven Kelk, Celine Scornavacca
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r…
A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees
Leo van Iersel, Steven Kelk, Nela Lekić +1
Reticulate events play an important role in determining evolutionary relationships. The problem of computing the minimum number of such events to explain discordance between two ph…
Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set
Steven Kelk, Leo van Iersel, Nela Lekic +3
We show that the problem of computing the hybridization number of two rooted binary phylogenetic trees on the same set of taxa X has a constant factor polynomial-time approximation…
A first step towards computing all hybridization networks for two rooted binary phylogenetic trees
Celine Scornavacca, Simone Linz, Benjamin Albrecht
Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimu…
Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable
Steven Kelk, Celine Scornavacca
Here we show that, given a set of clusters C on a set of taxa X, where |X|=n, it is possible to determine in time f(k).poly(n) whether there exists a level-<= k network (i.e. a net…