
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.





Philippe Gambette,
Katharina Huber and
Guillaume Scholz. Uprooted Phylogenetic Networks. In BMB, Vol. 79(9):20222048, 2017. Keywords: circular split system, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness. Note: http://arxiv.org/abs/1511.08387.







Katharina Huber,
Vincent Moulton,
Mike Steel and
Taoyang Wu. Folding and unfolding phylogenetic trees and networks. In JOMB, Vol. 73(6):17611780, 2016. Keywords: compressed network, explicit network, FUstable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network. Note: http://arxiv.org/abs/1506.04438.







Katharina Huber,
Leo van Iersel,
Vincent Moulton and
Taoyang Wu. How much information is needed to infer reticulate evolutionary histories? In Systematic Biology, Vol. 64(1):102111, 2015. Keywords: explicit network, from network, from rooted trees, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://dx.doi.org/10.1093/sysbio/syu076.



Katharina Huber and
Vincent Moulton. Encoding and Constructing 1Nested Phylogenetic Networks with Trinets. In ALG, Vol. 66(3):714738, 2013. Keywords: explicit network, from trinets, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://arxiv.org/abs/1110.0728.
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"Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or nontreelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from biological data using triplets, i.e. binary phylogenetic trees on 3element subsets of a given set of species. However, a fundamental problem with this approach is that the triplets displayed by a phylogenetic network do not necessarily uniquely determine or encode the network. Here we propose an alternative approach to encoding and constructing phylogenetic networks, which uses phylogenetic networks on 3element subsets of a set, or trinets, rather than triplets. More specifically, we show that for a special, wellstudied type of phylogenetic network called a 1nested network, the trinets displayed by a 1nested network always encode the network. We also present an efficient algorithm for deciding whether a dense set of trinets (i.e. one that contains a trinet on every 3element subset of a set) can be displayed by a 1nested network or not and, if so, constructs that network. In addition, we discuss some potential new directions that this new approach opens up for constructing and comparing phylogenetic networks. © 2012 Springer Science+Business Media, LLC."



Philippe Gambette and
Katharina Huber. On Encodings of Phylogenetic Networks of Bounded Level. In JOMB, Vol. 65(1):157180, 2012. Keywords: characterization, explicit network, from clusters, from rooted trees, from triplets, galled tree, identifiability, level k phylogenetic network, phylogenetic network, uniqueness, weak hierarchy. Note: http://hal.archivesouvertes.fr/hal00609130/en/.
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"Phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the wellstudied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i. e. uniquely describe) the network that induces it? For the large class of level1 (phylogenetic) networks we characterize those level1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. In addition, we show that three known distance measures for comparing phylogenetic networks are in fact metrics on the resulting subclass and give the diameter for two of them. Finally, we investigate the related concept of indistinguishability and also show that many properties enjoyed by level1 networks are not satisfied by networks of higher level. © 2011 SpringerVerlag."



Katharina Huber,
Leo van Iersel,
Steven Kelk and
Radoslaw Suchecki. A Practical Algorithm for Reconstructing Level1 Phylogenetic Networks. In TCBB, Vol. 8(3):607620, 2011. Keywords: explicit network, from triplets, galled tree, generation, heuristic, phylogenetic network, phylogeny, Program LEV1ATHAN, Program Lev1Generator, reconstruction, software. Note: http://arxiv.org/abs/0910.4067.
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"Recently, much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here, we present an efficient, practical algorithm for reconstructing level1 phylogenetic networksa type of network slightly more general than a phylogenetic treefrom triplets. Our algorithm has been made publicly available as the program Lev1athan. It combines ideas from several known theoretical algorithms for phylogenetic tree and network reconstruction with two novel subroutines. Namely, an exponentialtime exact and a greedy algorithm both of which are of independent theoretical interest. Most importantly, Lev1athan runs in polynomial time and always constructs a level1 network. If the data are consistent with a phylogenetic tree, then the algorithm constructs such a tree. Moreover, if the input triplet set is dense and, in addition, is fully consistent with some level1 network, it will find such a network. The potential of Lev1athan is explored by means of an extensive simulation study and a biological data set. One of our conclusions is that Lev1athan is able to construct networks consistent with a high percentage of input triplets, even when these input triplets are affected by a low to moderate level of noise. © 2011 IEEE."



Jaroslaw Byrka,
Pawel Gawrychowski,
Katharina Huber and
Steven Kelk. Worstcase optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. In Journal of Discrete Algorithms, Vol. 8(1):6575, 2010. Keywords: approximation, explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/0710.3258.
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"The study of phylogenetic networks is of great interest to computational evolutionary biology and numerous different types of such structures are known. This article addresses the following question concerning rooted versions of phylogenetic networks. What is the maximum value of p ∈ [0, 1] such that for every input set T of rooted triplets, there exists some network N such that at least p  T  of the triplets are consistent with N? We call an algorithm that computes such a network (where p is maximum) worstcase optimal. Here we prove that the set containing all triplets (the full triplet set) in some sense defines p. Moreover, given a network N that obtains a fraction p′ for the full triplet set (for any p′), we show how to efficiently modify N to obtain a fraction ≥ p′ for any given triplet set T. We demonstrate the power of this insight by presenting a worstcase optimal result for level1 phylogenetic networks improving considerably upon the 5/12 fraction obtained recently by Jansson, Nguyen and Sung. For level2 phylogenetic networks we show that p ≥ 0.61. We emphasize that, because we are taking  T  as a (trivial) upper bound on the size of an optimal solution for each specific input T, the results in this article do not exclude the existence of approximation algorithms that achieve approximation ratio better than p. Finally, we note that all the results in this article also apply to weighted triplet sets. © 2009 Elsevier B.V. All rights reserved."



Stefan Grünewald,
Katharina Huber,
Vincent Moulton,
Charles Semple and
Andreas Spillner. Characterizing weak compatibility in terms of weighted quartets. In Advances in Applied Mathematics, Vol. 42(3):329341, 2009. Keywords: abstract network, characterization, from quartets, split network, weak hierarchy. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/GHMSS08.pdf, slides at http://www.lirmm.fr/miep08/slides/12_02_huber.pdf.



Martin Lott,
Andreas Spillner,
Katharina Huber and
Vincent Moulton. PADRE: A Package for Analyzing and Displaying Reticulate Evolution. In BIO, Vol. 25(9):11991200, 2009. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software. Note: http://dx.doi.org/10.1093/bioinformatics/btp133.
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"Recent advances in gene sequencing for polyploid species, coupled with standard phylogenetic tree reconstruction, leads to gene trees in which the same species can label several leaves. Such multilabeled trees are then used to reconstruct the evolutionary history of the polyploid species in question. However, this reconstruction process requires new techniques that are not available in current phylogenetic software packages. Here, we describe the software package PADRE (Package for Analyzing and Displaying Reticulate Evolution) that implements such techniques, allowing the reconstruction of complex evolutionary histories for polyploids in the form of phylogenetic networks. © The Author 2009. Published by Oxford University Press. All rights reserved."



Martin Lott,
Andreas Spillner,
Katharina Huber,
Anna Petri,
Bengt Oxelman and
Vincent Moulton. Inferring polyploid phylogenies from multiplylabeled gene trees. In BMCEB, Vol. 9:216, 2009. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction. Note: http://dx.doi.org/10.1186/147121489216.
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"Background : Gene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiplylabeled, that is, the same leaf label can occur several times in a single tree. This property considerably complicates the task of forming a consensus of a collection of such trees compared to usual phylogenetic trees. Results. We present a method for computing a consensus tree of multiplylabeled trees. As with the wellknown greedy consensus tree approach for phylogenetic trees, our method first breaks the given collection of gene trees into a set of clusters. It then aims to insert these clusters one at a time into a tree, starting with the clusters that are supported by most of the gene trees. As the problem to decide whether a cluster can be inserted into a multiplylabeled tree is computationally hard, we have developed a heuristic method for solving this problem. Conclusion. We illustrate the applicability of our method using two collections of trees for plants of the genus Silene, that involve several allopolyploids at different levels. © 2009 Lott et al; licensee BioMed Central Ltd."



Stefan Grünewald,
Katharina Huber and
Qiong Wu. Two novel closure rules for constructing phylogenetic supernetworks. In BMB, Vol. 70(7):19061924, 2008. Keywords: abstract network, from splits, from unrooted trees, phylogenetic network, phylogeny, Program MY CLOSURE, reconstruction, supernetwork. Note: http://arxiv.org/abs/0709.0283, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/huber/.
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"A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection P of partial trees (leaflabeled trees whose leaves are bijectively labeled by species or, more generally, taxa, each supported by, e.g., a gene) into an overall parental structure that displays all trees in P. This already difficult problem is complicated by the fact that the trees in P regularly support conflicting phylogenetic relationships and are not on the same but only overlapping taxa sets. A desirable requirement on the sought after parental structure, therefore, is that it can accommodate the observed conflicts. Phylogenetic networks are a popular tool capable of doing precisely this. However, not much is known about how to construct such networks from partial trees, a notable exception being the Zclosure supernetwork approach, which is based on the Zclosure rule, and the Qimputation approach. Although attractive approaches, they both suffer from the fact that the generated networks tend to be multidimensional making it necessary to apply some kind of filter to reduce their complexity. To avoid having to resort to a filter, we follow a different line of attack in this paper and develop closure rules for generating circular phylogenetic networks which have the attractive property that they can be represented in the plane. In particular, we introduce the novel Y(closure) rule and show that this rule on its own or in combination with one of Meacham's closure rules (which we call the Mrule) has some very desirable theoretical properties. In addition, we present a case study based on Rivera et al. "ring of life" to explore the reconstructive power of the M and Yrule and also reanalyze an Arabidopsis thaliana data set. © 2008 Society for Mathematical Biology."



Andreas W. M. Dress,
Katharina Huber,
Jacobus Koolen and
Vincent Moulton. Compatible decompositions and block realizations of finite metrics. In EJC, Vol. 29(7):16171633, 2008. Keywords: abstract network, block realization, from distances, phylogenetic network, phylogeny, realization, reconstruction. Note: http://www.ims.nus.edu.sg/preprints/200721.pdf.
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"Given a metric D defined on a finite set X, we define a finite collection D of metrics on X to be a compatible decomposition of D if any two distinct metrics in D are linearly independent (considered as vectors in RX × X), D = ∑d ∈ D d holds, and there exist points x, x′ ∈ X for any two distinct metrics d, d′ in D such that d (x, y) d′ (x′, y) = 0 holds for every y ∈ X. In this paper, we show that such decompositions are in onetoone correspondence with (isomorphism classes of) block realizations of D, that is, graph realizations G of D for which G is a block graph and for which every vertex in G not labelled by X has degree at least 3 and is a cut point of G. This generalizes a fundamental result in phylogenetic combinatorics that states that a metric D defined on X can be realized by a tree if and only if there exists a compatible decomposition D of D such that all metrics d ∈ D are split metrics, and lays the foundation for a more general theory of metric decompositions that will be explored in future papers. © 2007 Elsevier Ltd. All rights reserved."



Barbara R. Holland,
Steffi Benthin,
Peter J. Lockhart,
Vincent Moulton and
Katharina Huber. Using supernetworks to distinguish hybridization from lineagesorting. In BMCEB, Vol. 8(202), 2008. Keywords: explicit network, from unrooted trees, hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, supernetwork. Note: http://dx.doi.org/10.1186/147121488202.
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"Background. A simple and widely used approach for detecting hybridization in phylogenies is to reconstruct gene trees from independent gene loci, and to look for gene tree incongruence. However, this approach may be confounded by factors such as poor taxonsampling and/or incomplete lineagesorting. Results. Using coalescent simulations, we investigated the potential of supernetwork methods to differentiate between gene tree incongruence arising from taxon sampling and incomplete lineagesorting as opposed to hybridization. For few hybridization events, a large number of independent loci, and wellsampled taxa across these loci, we found that it was possible to distinguish incomplete lineagesorting from hybridization using the filtered Zclosure and Qimputation supernetwork methods. Moreover, we found that the choice of supernetwork method was less important than the choice of filtering, and that countbased filtering was the most effective filtering technique. Conclusion. Filtered supernetworks provide a tool for detecting and identifying hybridization events in phylogenies, a tool that should become increasingly useful in light of current genome sequencing initiatives and the ease with which large numbers of independent gene loci can be determined using new generation sequencing technologies. © 2008 Holland et al; licensee BioMed Central Ltd."



Barbara R. Holland,
Glenn Conner,
Katharina Huber and
Vincent Moulton. Imputing Supertrees and Supernetworks from Quartets. In Systematic Biology, Vol. 56(1):5767, 2007. Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program Quartet, reconstruction, split network, supernetwork. Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.99.3215.
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"Inferring species phylogenies is an important part of understanding molecular evolution. Even so, it is well known that an accurate phylogenetic tree reconstruction for a single gene does not always necessarily correspond to the species phylogeny. One commonly accepted strategy to cope with this problem is to sequence many genes; the way in which to analyze the resulting collection of genes is somewhat more contentious. Supermatrix and supertree methods can be used, although these can suppress conflicts arising from true differences in the gene trees caused by processes such as lineage sorting, horizontal gene transfer, or gene duplication and loss. In 2004, Huson et al. (IEEE/ACM Trans. Comput. Biol. Bioinformatics 1:151158) presented the Zclosure method that can circumvent this problem by generating a supernetwork as opposed to a supertree. Here we present an alternative way for generating supernetworks called Qimputation. In particular, we describe a method that uses quartet information to add missing taxa into gene trees. The resulting trees are subsequently used to generate consensus networks, networks that generalize strict and majorityrule consensus trees. Through simulations and application to real data sets, we compare Qimputation to the matrix representation with parsimony (MRP) supertree method and Zclosure, and demonstrate that it provides a useful complementary tool. Copyright © Society of Systematic Biologists."



Katharina Huber,
Bengt Oxelman,
Martin Lott and
Vincent Moulton. Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees. In MBE, Vol. 23(9):17841791, 2007. Keywords: duplication, explicit network, from multilabeled tree, from trees, phylogenetic network, phylogeny, Program PADRE, reconstruction, software. Note: http://mbe.oxfordjournals.org/cgi/content/full/23/9/1784.
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"In recent studies, phylogenetic networks have been derived from socalled multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/ ∼a043878/padre.html. © The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved."



Vincent Moulton and
Katharina Huber. Phylogenetic networks from multilabelled trees. In JOMB, Vol. 52(5):613632, 2006. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction. Note: http://www.uea.ac.uk/~a043878/jmb.pdf.
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"It is now quite well accepted that the evolutionary past of certain species is better represented by phylogenetic networks as opposed to trees. For example, polyploids are typically thought to have resulted through hybridization and duplication, processes that are probably not best represented as bifurcating speciation events. Based on the knowledge of a multilabelled tree relating collection of polyploids, we present a canonical construction of a phylogenetic network that exhibits the tree. In addition, we prove that the resulting network is in some welldefined sense a minimal network having this property. © SpringerVerlag 2006."



Katharina Huber,
Vincent Moulton and
Charles Semple. Replacing cliques by stars in quasimedian graphs. In DAM, Vol. 143(13), 2004. Note: http://dx.doi.org/10.1016/j.dam.2004.03.002.
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"For a multiset Σ of splits (bipartitions) of a finite set X, we introduce the multisplit graph G(Σ). This graph is a natural extension of the Buneman graph, Indeed, it is shown that several results pertaining to the Buneman graph extend to the multisplit graph. In addition, in case Σ is derived from a set ℛ of partitions of X by taking parts together with their complements, we show that the extremal instances where ℛ is either strongly compatible or strongly incompatible are equivalent to G(Σ) being either a tree or a Cartesian product of star trees, respectively. © 2004 Elsevier B.V. All rights reserved."



Katharina Huber,
Michael Langton,
David Penny,
Vincent Moulton and
Mike Hendy. Spectronet: A package for computing spectra and median networks. In ABIO, Vol. 1(3):159161, 2004. Keywords: from splits, median network, phylogenetic network, phylogeny, Program Spectronet, software, split, visualization. Note: http://citeseer.ist.psu.edu/631776.html.
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Spectronet is a package that uses various methods for exploring and visualising complex evolutionary signals. Given an alignment in NEXUS format, the package works by computing a collection of weighted splits or bipartitions of the taxa and then allows the user to interactively analyse the resulting collection using tools such as Lentoplots and median networks. The package is highly interactive and available for PCs.





Katharina Huber,
Vincent Moulton,
Peter J. Lockhart and
Andreas W. M. Dress. Pruned Median Networks: A Technique for Reducing the Complexity of Median Networks. In MPE, Vol. 19(2):302310, 2001. Keywords: abstract network, median network, phylogenetic network, phylogeny, split. Note: http://dx.doi.org/10.1006/mpev.2001.0935.
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"Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by treelike bifurcating evolutionary models. These observations might result from processes of species diversification and/or processes of sequence evolution that are not treelike. In these cases, bifurcating tree representations provide poor visualization of phylogenetic signals in sequence data. In this paper, we use median networks to study DNA sequence substitution patterns in plant nuclear and chloroplast markers. We describe how to prune median networks to obtain so called pruned median networks. These simpler networks may help to provide a useful framework for investigating the phylogenetic complexity of recently diverged taxa with hybrid origins. © 2001 Academic Press."



Katharina Huber,
Elizabeth E. Watson and
Mike Hendy. An Algorithm for Constructing Local Regions in a Phylogenetic Network. In MPE, Vol. 19(1):18, 2000. Keywords: abstract network, median network, phylogenetic network, phylogeny, reconstruction, split. Note: http://dx.doi.org/10.1006/mpev.2000.0891.
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"The groupings of taxa in a phylogenetic tree cannot represent all the conflicting signals that usually occur among site patterns in aligned homologous genetic sequences. Hence a treebuilding program must compromise by reporting a subset of the patterns, using some discriminatory criterion. Thus, in the worst case, out of possibly a large number of equally good trees, only an arbitrarily chosen tree might be reported by the treebuilding program as" The Tree." This tree might then be used as a basis for phylogenetic conclusions. One strategy to represent conflicting patterns in the data is to construct a network. The Buneman graph is a theoretically very attractive example of such a network. In particular, a characterization for when this network will be a tree is known. Also the Buneman graph contains each of the most parsimonious trees indicated by the data. In this paper we describe a new method for constructing the Buneman graph that can be used for a generalization of Hadamard conjugation to networks. This new method differs from previous methods by allowing us to focus on local regions of the graph without having to first construct the full graph. The construction is illustrated by an example. © 2001 Academic Press."







