




Katharina Huber,
Leo van Iersel,
Vincent Moulton,
Celine Scornavacca and
Taoyang Wu. Reconstructing phylogenetic level1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173200, 2017. Keywords: explicit network, FPT, from binets, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://arxiv.org/abs/1411.6804.






Steven Kelk,
Leo van Iersel,
Celine Scornavacca and
Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. In JGAA, Vol. 20(2):189215, 2016. Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction. Note: http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf.



Vincent Ranwez,
Celine Scornavacca,
JeanPhilippe Doyon and
Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. In JOMB, Vol. 72(7):18111844, 2016. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.



François Chevenet,
JeanPhilippe Doyon,
Celine Scornavacca,
Edwin Jacox,
Emmanuelle Jousselin and
Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608610, 2016. Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization. Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.





Philippe Gambette,
Leo van Iersel,
Steven Kelk,
Fabio Pardi and
Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):17731795, 2016. Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudopolynomial, time consistent network, tree containment, tree sibling network. Note: http://arxiv.org/abs/1607.06285.






Mareike Fischer,
Leo van Iersel,
Steven Kelk and
Celine Scornavacca. On Computing The Maximum Parsimony Score Of A Phylogenetic Network. In SIDMA, Vol. 29(1):559585, 2015. Keywords: APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software. Note: http://arxiv.org/abs/1302.2430.










Steven Kelk and
Celine Scornavacca. Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable. In ALG, Vol. 68(4):886915, 2014. Keywords: explicit network, FPT, from clusters, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/1108.3653.
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"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 network where each biconnected component has reticulation number at most k) that represents all the clusters in C in the softwired sense, and if so to construct such a network. This extends a result from Kelk et al. (in IEEE/ACM Trans. Comput. Biol. Bioinform. 9:517534, 2012) which showed that the problem is polynomialtime solvable for fixed k. By defining "kreticulation generators" analogous to "levelk generators", we then extend this fixed parameter tractability result to the problem where k refers not to the level but to the reticulation number of the whole network. © 2012 Springer Science+Business Media New York."



Leo van Iersel,
Steven Kelk,
Nela Lekic and
Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees. In BMCB, Vol. 15(127):112, 2014. Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, Program CycleKiller, Program TerminusEst, reconstruction. Note: http://dx.doi.org/10.1186/1471210515127.








Celine Scornavacca,
Paprotny Wojciech,
Vincent Berry and
Vincent Ranwez. Representing a set of reconciliations in a compact way. In JBCB, Vol. 11(2):1250025, 2013. Keywords: duplication, explicit network, from network, from rooted trees, from species tree, phylogeny, Program GraphDTL, Program TERA, visualization. Note: http://hallirmm.ccsd.cnrs.fr/lirmm00818801.
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"Comparative genomic studies are often conducted by reconciliation analyses comparing gene and species trees. One of the issues with reconciliation approaches is that an exponential number of optimal scenarios is possible. The resulting complexity is masked by the fact that a majority of reconciliation software pick up a random optimal solution that is returned to the enduser. However, the alternative solutions should not be ignored since they tell different stories that parsimony considers as viable as the output solution. In this paper, we describe a polynomial space and time algorithm to build a minimum reconciliation grapha graph that summarizes the set of all most parsimonious reconciliations. Amongst numerous applications, it is shown how this graph allows counting the number of nonequivalent most parsimonious reconciliations. © 2013 Imperial College Press."



ThiHau Nguyen,
Vincent Ranwez,
Vincent Berry and
Celine Scornavacca. Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods. In PLoS ONE, Vol. 8(10):e73667, 2013. Keywords: duplication, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, Program GraphDTL, reconstruction. Note: http://dx.doi.org/10.1371/journal.pone.0073667.
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"The genome content of extant species is derived from that of ancestral genomes, distorted by evolutionary events such as gene duplications, transfers and losses. Reconciliation methods aim at recovering such events and at localizing them in the species history, by comparing gene family trees to species trees. These methods play an important role in studying genome evolution as well as in inferring orthology relationships. A major issue with reconciliation methods is that the reliability of predicted evolutionary events may be questioned for various reasons: Firstly, there may be multiple equally optimal reconciliations for a given species treegene tree pair. Secondly, reconciliation methods can be misled by inaccurate gene or species trees. Thirdly, predicted events may fluctuate with method parameters such as the cost or rate of elementary events. For all of these reasons, confidence values for predicted evolutionary events are sorely needed. It was recently suggested that the frequency of each event in the set of all optimal reconciliations could be used as a support measure. We put this proposition to the test here and also consider a variant where the support measure is obtained by additionally accounting for suboptimal reconciliations. Experiments on simulated data show the relevance of event supports computed by both methods, while resorting to suboptimal sampling was shown to be more effective. Unfortunately, we also show that, unlike the majorityrule consensus tree for phylogenies, there is no guarantee that a single reconciliation can contain all events having above 50% support. In this paper, we detail how to rely on the reconciliation graph to efficiently identify the median reconciliation. Such median reconciliation can be found in polynomial time within the potentially exponential set of most parsimonious reconciliations. © 2013 Nguyen et al."








Steven Kelk,
Celine Scornavacca and
Leo van Iersel. On the elusiveness of clusters. In TCBB, Vol. 9(2):517534, 2012. Keywords: explicit network, from clusters, from rooted trees, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, Program Clustistic, reconstruction, software. Note: http://arxiv.org/abs/1103.1834.



Celine Scornavacca,
Simone Linz and
Benjamin Albrecht. A first step towards computing all hybridization networks for two rooted binary phylogenetic trees. In JCB, Vol. 19:12271242, 2012. Keywords: agreement forest, explicit network, FPT, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction. Note: http://arxiv.org/abs/1109.3268.
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"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 minimum number of hybridization vertices. With the standard app1235roach to tackle this problem being combinatorial, the reconstructed network is rarely unique. From a biological point of view, it is therefore of importance to not only compute one network, but all possible networks. In this article, we make a first step toward approaching this goal by presenting the first algorithmcalled allMAAFsthat calculates all maximumacyclicagreement forests for two rooted binary phylogenetic trees on the same set of taxa. © Copyright 2012, Mary Ann Liebert, Inc. 2012."



Benjamin Albrecht,
Celine Scornavacca,
Alberto Cenci and
Daniel H. Huson. Fast computation of minimum hybridization networks. In BIO, Vol. 28(2):191197, 2012. Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction. Note: http://dx.doi.org/10.1093/bioinformatics/btr618.
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"Motivation: Hybridization events in evolution may lead to incongruent gene trees. One approach to determining possible interspecific hybridization events is to compute a hybridization network that attempts to reconcile incongruent gene trees using a minimum number of hybridization events. Results: We describe how to compute a representative set of minimum hybridization networks for two given bifurcating input trees, using a parallel algorithm and provide a userfriendly implementation. A simulation study suggests that our program performs significantly better than existing software on biologically relevant data. Finally, we demonstrate the application of such methods in the context of the evolution of the Aegilops/Triticum genera. Availability and implementation: The algorithm is implemented in the program Dendroscope 3, which is freely available from www.dendroscope.org and runs on all three major operating systems. © The Author 2011. Published by Oxford University Press. All rights reserved."



Steven Kelk,
Leo van Iersel,
Nela Lekic,
Simone Linz,
Celine Scornavacca and
Leen Stougie. Cycle killer... qu'estce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set. In SIDMA, Vol. 26(4):16351656, 2012. Keywords: agreement forest, approximation, explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CycleKiller, reconstruction. Note: http://arxiv.org/abs/1112.5359, about the title.
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"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 polynomialtime approximation if and only if the problem of computing a minimumsize feedback vertex set in a directed graph (DFVS) has a constant factor polynomialtime approximation. The latter problem, which asks for a minimum number of vertices to be removed from a directed graph to transform it into a directed acyclic graph, is one of the problems in Karp's seminal 1972 list of 21 NPcomplete problems. Despite considerable attention from the combinatorial optimization community, it remains to this day unknown whether a constant factor polynomialtime approximation exists for DFVS. Our result thus places the (in)approximability of hybridization number in a much broader complexity context, and as a consequence we obtain that it inherits inapproximability results from the problem Vertex Cover. On the positive side, we use results from the DFVS literature to give an O(log r log log r) approximation for the hybridization number where r is the correct value. Copyright © by SIAM."



Leo van Iersel,
Steven Kelk,
Nela Lekic and
Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number. In WABI12, Vol. 7534(430440) of LNCS, springer, 2012. Keywords: agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software. Note: http://arxiv.org/abs/1205.3417.
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"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 phylogenetic trees is a hard computational problem. In practice, exact solvers struggle to solve instances with reticulation number larger than 40. For such instances, one has to resort to heuristics and approximation algorithms. Here we present the algorithm CycleKiller which is the first approximation algorithm that can produce solutions verifiably close to optimality for instances with hundreds or even thousands of reticulations. Theoretically, the algorithm is an exponentialtime 2approximation (or 4approximation in its fastest mode). However, using simulations we demonstrate that in practice the algorithm runs quickly for large and difficult instances, producing solutions within one percent of optimality. An implementation of this algorithm, which extends the theoretical work of [14], has been made publicly available. © 2012 SpringerVerlag."



Daniel H. Huson and
Celine Scornavacca. Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. In Systematic Biology, Vol. 61(6):10611067, 2012. Keywords: from rooted trees, from triplets, phylogenetic network, phylogeny, Program Dendroscope, reconstruction, software, visualization.
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"Dendroscope 3 is a new program for working with rooted phylogenetic trees and networks. It provides a number of methods for drawing and comparing rooted phylogenetic networks, and for computing them from rooted trees. The program can be used interactively or in commandline mode. The program is written in Java, use of the software is free, and installers for all 3 major operating systems can be downloaded from www.dendroscope.org. [Phylogenetic trees; phylogenetic networks; software.] © 2012 The Author(s)."








Daniel H. Huson and
Celine Scornavacca. A survey of combinatorial methods for phylogenetic networks. In Genome Biology and Evolution, Vol. 3:2335, 2011. Keywords: phylogenetic network, survey. Note: http://dx.doi.org/10.1093/gbe/evq077.
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"The evolutionary history of a set of species is usually described by a rooted phylogenetic tree. Although it is generally undisputed that bifurcating speciation events and descent with modifications are major forces of evolution, there is a growing belief that reticulate events also have a role to play. Phylogenetic networks provide an alternative to phylogenetic trees and may be more suitable for data sets where evolution involves significant amounts of reticulate events, such as hybridization, horizontal gene transfer, or recombination. In this article, we give an introduction to the topic of phylogenetic networks, very briefly describing the fundamental concepts and summarizing some of the most important combinatorial methods that are available for their computation. © 2010 The Author(s)."





JeanPhilippe Doyon,
Celine Scornavacca,
Konstantin Yu Gorbunov,
Gergely J. Szöllösi,
Vincent Ranwez and
Vincent Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications, and transfers. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMBCG'10), Vol. 6398:93108 of LNCS, springer, 2011. Keywords: branch length, duplication, dynamic programming, explicit network, from multilabeled tree, from species tree, from unrooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Mowgli, reconstruction. Note: http://www.lirmm.fr/~vberry/Publis/MPRDoyonEtAl.pdf, software available at http://www.atgcmontpellier.fr/MPR/.
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"Tree reconciliation methods aim at estimating the evolutionary events that cause discrepancy between gene trees and species trees. We provide a discrete computational model that considers duplications, transfers and losses of genes. The model yields a fast and exact algorithm to infer time consistent and most parsimonious reconciliations. Then we study the conditions under which parsimony is able to accurately infer such events. Overall, it performs well even under realistic rates, transfers being in general less accurately recovered than duplications. An implementation is freely available at http://www.atgc montpellier.fr/MPR. © 2010 SpringerVerlag."



Celine Scornavacca,
Franziska Zickmann and
Daniel H. Huson. Tanglegrams for Rooted Phylogenetic Trees and Networks. In ISMB11, Vol. 27(13):i248i256 of BIO, 2011. Keywords: from network, heuristic, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization. Note: http://dx.doi.org/10.1093/bioinformatics/btr210.
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"Motivation: In systematic biology, one is often faced with the task of comparing different phylogenetic trees, in particular in multigene analysis or cospeciation studies. One approach is to use a tanglegram in which two rooted phylogenetic trees are drawn opposite each other, using auxiliary lines to connect matching taxa. There is an increasing interest in using rooted phylogenetic networks to represent evolutionary history, so as to explicitly represent reticulate events, such as horizontal gene transfer, hybridization or reassortment. Thus, the question arises how to define and compute a tanglegram for such networks. Results: In this article, we present the first formal definition of a tanglegram for rooted phylogenetic networks and present a heuristic approach for computing one, called the NNtanglegram method. We compare the performance of our method with existing tree tanglegram algorithms and also show a typical application to real biological datasets. For maximum usability, the algorithm does not require that the trees or networks are bifurcating or bicombining, or that they are on identical taxon sets. © The Author(s) 2011. Published by Oxford University Press."



