Who is Who in Phylogenetic Networks

Publications of Katharina Huber     Order by:   Type | Year

Associated keywords

abstract-network approximation block-realization bound cactus-graph characterization cherry-picking circular-split-system compressed-network consensus distance-between-networks duplication explicit-network exponential-algorithm FPT from-binets from-clusters from-distances from-multilabeled-tree from-network from-quarnets from-quartets from-rooted-trees from-splits from-subnetworks from-trees from-trinets from-triplets from-unrooted-trees FU-stable-network galled-tree generation heuristic hybridization identifiability level-k-phylogenetic-network lineage-sorting LST-distance median-network NNI-distance NNI-moves normal-network NP-complete optimal-realization orchard-network orientation phylogenetic-network phylogeny polynomial Program-LEV1ATHAN Program-Lev1Generator Program-MY-CLOSURE Program-PADRE Program-Quartet Program-Spectronet Program-SplitsTree realization reconstruction rigidly-displaying software split split-network SPR-distance stack-free-network supernetwork survey TBR-distance time-consistent-network tree-containment tree-sibling-network tree-based-network tree-child-network uniqueness unrooted-tree-based-network valid-network visualization weak-hierarchy weakly-displaying

Article (Journal)

1 Katharina Huber and Guillaume Scholz. Phylogenetic networks that are their own fold-ups. In AAM, Vol. 113(101959):1-24, 2020. Keywords: characterization, explicit network, FU-stable network, phylogenetic network, phylogeny. Note: https://arxiv.org/abs/1804.01841.         2 Momoko Hayamizu, Katharina Huber, Vincent Moulton and Yukihiro Murakami. Recognizing and realizing cactus metrics. In IPL, Vol. 157(105916):1-5, 2020. Keywords: cactus graph, from distances, level k phylogenetic network, optimal realization, polynomial. Note: https://doi.org/10.1016/j.ipl.2020.105916.         3 Katharina Huber, Vincent Moulton and Taoyang Wu. Hierarchies from lowest stable ancestors in nonbinary phylogenetic networks. In JOC, Vol. 36:200-231, 2019. Keywords: characterization, explicit network, phylogenetic network, phylogeny. Note: https://link.springer.com/content/pdf/10.1007/s00357-018-9279-5.pdf.         4 Andrew R. Francis, Katharina Huber, Vincent Moulton and Taoyang Wu. Bounds for phylogenetic network space metrics. In JOMB, Vol. 76(5):1229-1248, 2018. Keywords: bound, distance between networks, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance, TBR distance. Note: https://arxiv.org/abs/1702.05609.         5 Andrew R. Francis, Katharina Huber and Vincent Moulton. Tree-based unrooted phylogenetic networks. In BMB, Vol. 80(2):404-416, 2018. Keywords: characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree containment, tree-based network, unrooted tree-based network. Note: https://arxiv.org/abs/1704.02062.         6 Katharina Huber, Vincent Moulton, Charles Semple and Taoyang Wu. Quarnet inference rules for level-1 networks. In BMB, Vol. 80:2137-2153, 2018. Keywords: explicit network, from quarnets, from subnetworks, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: https://arxiv.org/abs/1711.06720.         7 Magnus Bordewich, Katharina Huber, Vincent Moulton and Charles Semple. Recovering normal networks from shortest inter-taxa distance information. In JOMB, Vol. 77(3):571-594, 2018. Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, uniqueness. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BHMS18.pdf.         8 Katharina Huber, Leo van Iersel, Vincent Moulton, Celine Scornavacca and Taoyang Wu. Reconstructing phylogenetic level-1 networks from nondense binet and trinet sets. In ALG, Vol. 77(1):173-200, 2017. Keywords: explicit network, FPT, from binets, from subnetworks, from trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://arxiv.org/abs/1411.6804.         9 Philippe Gambette, Katharina Huber and Steven Kelk. On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters. In JOMB, Vol. 74(7):1729-1751, 2017. Keywords: from clusters, from triplets, galled tree, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://dx.doi.org/10.1007/s00285-016-1068-3.         10 Philippe Gambette, Katharina Huber and Guillaume Scholz. Uprooted Phylogenetic Networks. In BMB, Vol. 79(9):2022-2048, 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.         11 Katharina Huber, Vincent Moulton, Mike Steel and Taoyang Wu. Folding and unfolding phylogenetic trees and networks. In JOMB, Vol. 73(6):1761-1780, 2016. Keywords: compressed network, explicit network, FU-stable network, NP complete, phylogenetic network, phylogeny, tree containment, tree sibling network. Note: http://arxiv.org/abs/1506.04438.         12 Katharina Huber, Simone Linz, Vincent Moulton and Taoyang Wu. Spaces of phylogenetic networks from generalized nearest-neighbor interchange operations. In JOMB, Vol. 72(2):699-725, 2016. Keywords: bound, distance between networks, from network, LST distance, phylogenetic network, phylogeny.         13 Katharina Huber, Vincent Moulton and Taoyang Wu. Transforming phylogenetic networks: Moving beyond tree space. In JTB, Vol. 404:30-39, 2016. Keywords: distance between networks, level k phylogenetic network, NNI moves, phylogenetic network, phylogeny. Note: http://arxiv.org/abs/1601.01788.         14 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):102-111, 2015. Keywords: explicit network, from network, from rooted trees, from subnetworks, from trinets, identifiability, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://dx.doi.org/10.1093/sysbio/syu076.         15 Katharina Huber and Vincent Moulton. Encoding and Constructing 1-Nested Phylogenetic Networks with Trinets. In ALG, Vol. 66(3):714-738, 2013. Keywords: explicit network, from subnetworks, from trinets, phylogenetic network, phylogeny, reconstruction, uniqueness. Note: http://arxiv.org/abs/1110.0728.         Toggle abstract "Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from biological data using triplets, i.e. binary phylogenetic trees on 3-element 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 3-element subsets of a set, or trinets, rather than triplets. More specifically, we show that for a special, well-studied type of phylogenetic network called a 1-nested network, the trinets displayed by a 1-nested 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 3-element subset of a set) can be displayed by a 1-nested 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." 16 Philippe Gambette and Katharina Huber. On Encodings of Phylogenetic Networks of Bounded Level. In JOMB, Vol. 65(1):157-180, 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.archives-ouvertes.fr/hal-00609130/en/.         Toggle abstract "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 well-studied 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 level-1 (phylogenetic) networks we characterize those level-1 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 level-1 networks are not satisfied by networks of higher level. © 2011 Springer-Verlag." 17 Katharina Huber, Leo van Iersel, Steven Kelk and Radoslaw Suchecki. A Practical Algorithm for Reconstructing Level-1 Phylogenetic Networks. In TCBB, Vol. 8(3):607-620, 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.         Toggle abstract "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 level-1 phylogenetic networks-a type of network slightly more general than a phylogenetic tree-from 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 exponential-time exact and a greedy algorithm both of which are of independent theoretical interest. Most importantly, Lev1athan runs in polynomial time and always constructs a level-1 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 level-1 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." 18 Jaroslaw Byrka, Pawel Gawrychowski, Katharina Huber and Steven Kelk. Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks. In Journal of Discrete Algorithms, Vol. 8(1):65-75, 2010. Keywords: approximation, explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction. Note: http://arxiv.org/abs/0710.3258.         Toggle abstract "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) worst-case 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 worst-case optimal result for level-1 phylogenetic networks improving considerably upon the 5/12 fraction obtained recently by Jansson, Nguyen and Sung. For level-2 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." 19 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):329-341, 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.         20 Martin Lott, Andreas Spillner, Katharina Huber and Vincent Moulton. PADRE: A Package for Analyzing and Displaying Reticulate Evolution. In BIO, Vol. 25(9):1199-1200, 2009. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software. Note: http://dx.doi.org/10.1093/bioinformatics/btp133.         Toggle abstract "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 multi-labeled 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." 21 Martin Lott, Andreas Spillner, Katharina Huber, Anna Petri, Bengt Oxelman and Vincent Moulton. Inferring polyploid phylogenies from multiply-labeled 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/10.1186/1471-2148-9-216.         Toggle abstract "Background : Gene trees that arise in the context of reconstructing the evolutionary history of polyploid species are often multiply-labeled, 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 multiply-labeled trees. As with the well-known 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 multiply-labeled 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." 22 Stefan Grünewald, Katharina Huber and Qiong Wu. Two novel closure rules for constructing phylogenetic super-networks. In BMB, Vol. 70(7):1906-1924, 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/.         Toggle abstract "A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection P of partial trees (leaf-labeled 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 Z-closure super-network approach, which is based on the Z-closure rule, and the Q-imputation 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 M-rule) 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 Y-rule and also reanalyze an Arabidopsis thaliana data set. © 2008 Society for Mathematical Biology." 23 Andreas W. M. Dress, Katharina Huber, Jacobus Koolen and Vincent Moulton. Compatible decompositions and block realizations of finite metrics. In EJC, Vol. 29(7):1617-1633, 2008. Keywords: abstract network, block realization, from distances, phylogenetic network, phylogeny, realization, reconstruction. Note: http://www.ims.nus.edu.sg/preprints/2007-21.pdf.         Toggle abstract "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 one-to-one 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." 24 Barbara R. Holland, Steffi Benthin, Peter J. Lockhart, Vincent Moulton and Katharina Huber. Using supernetworks to distinguish hybridization from lineage-sorting. 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/10.1186/1471-2148-8-202.         Toggle abstract "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 taxon-sampling and/or incomplete lineage-sorting. Results. Using coalescent simulations, we investigated the potential of supernetwork methods to differentiate between gene tree incongruence arising from taxon sampling and incomplete lineage-sorting as opposed to hybridization. For few hybridization events, a large number of independent loci, and well-sampled taxa across these loci, we found that it was possible to distinguish incomplete lineage-sorting from hybridization using the filtered Z-closure and Q-imputation supernetwork methods. Moreover, we found that the choice of supernetwork method was less important than the choice of filtering, and that count-based 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." 25 Barbara R. Holland, Glenn Conner, Katharina Huber and Vincent Moulton. Imputing Supertrees and Supernetworks from Quartets. In Systematic Biology, Vol. 56(1):57-67, 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.         Toggle abstract "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 1:151-158) presented the Z-closure 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 Q-imputation. 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 majority-rule consensus trees. Through simulations and application to real data sets, we compare Q-imputation to the matrix representation with parsimony (MRP) supertree method and Z-closure, and demonstrate that it provides a useful complementary tool. Copyright © Society of Systematic Biologists." 26 Katharina Huber, Bengt Oxelman, Martin Lott and Vincent Moulton. Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees. In MBE, Vol. 23(9):1784-1791, 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.         Toggle abstract "In recent studies, phylogenetic networks have been derived from so-called 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." 27 Vincent Moulton and Katharina Huber. Phylogenetic networks from multi-labelled trees. In JOMB, Vol. 52(5):613-632, 2006. Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction. Note: http://www.uea.ac.uk/~a043878/jmb.pdf.         Toggle abstract "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 multi-labelled 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 well-defined sense a minimal network having this property. © Springer-Verlag 2006." 28 Katharina Huber, Vincent Moulton and Charles Semple. Replacing cliques by stars in quasi-median graphs. In DAM, Vol. 143(1-3), 2004. Note: http://dx.doi.org/10.1016/j.dam.2004.03.002.         Toggle abstract "For a multi-set Σ of splits (bipartitions) of a finite set X, we introduce the multi-split 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 multi-split 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." 29 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):159-161, 2004. Keywords: from splits, median network, phylogenetic network, phylogeny, Program Spectronet, software, split, visualization. Note: http://citeseer.ist.psu.edu/631776.html.         Toggle abstract 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 Lento-plots and median networks. The package is highly interactive and available for PCs. 30 Barbara R. Holland, Katharina Huber, Vincent Moulton and Peter J. Lockhart. Using consensus networks to visualize contradictory evidence for species phylogeny. In MBE, Vol. 21(7):1459-1461, 2004. Keywords: consensus, from trees, phylogenetic network, phylogeny, split, visualization. Note: http://dx.doi.org/10.1093/molbev/msh145.         Toggle abstract Building species phylogenies from genome data requires the evaluation of phylogenetic evidence from independent gene loci. We propose an approach to do this using consensus networks. We compare gene trees for eight yeast genomes and show that consensus networks have potential for helping to visualize contradictory evidence for species phylogenies. 31 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):302-310, 2001. Keywords: abstract network, median network, phylogenetic network, phylogeny, split. Note: http://dx.doi.org/10.1006/mpev.2001.0935.         Toggle abstract "Observations from molecular marker studies on recently diverged species indicate that substitution patterns in DNA sequences can often be complex and poorly described by tree-like bifurcating evolutionary models. These observations might result from processes of species diversification and/or processes of sequence evolution that are not tree-like. 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." 32 Katharina Huber, Elizabeth E. Watson and Mike Hendy. An Algorithm for Constructing Local Regions in a Phylogenetic Network. In MPE, Vol. 19(1):1-8, 2000. Keywords: abstract network, median network, phylogenetic network, phylogeny, reconstruction, split. Note: http://dx.doi.org/10.1006/mpev.2000.0891.         Toggle abstract "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 tree-building 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 tree-building 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." 33 Andreas W. M. Dress, Katharina Huber and Vincent Moulton. Some Variations on a Theme by Buneman. In ACOM, Vol. 1:339-352, 1997. Note: http://dx.doi.org/10.1007/BF02558485.         34 Andreas W. M. Dress, Mike Hendy, Katharina Huber and Vincent Moulton. On the number of vertices and edges in the Buneman graph. In ACOM, Vol. 1:329-337, 1997. Keywords: abstract network, median network, phylogenetic network, phylogeny, split. Note: http://dx.doi.org/10.1007/BF02558484.

InProceedings

35 Katharina Huber, Vincent Moulton, Andreas Spillner, Sabine Storandt and Radoslaw Suchecki. Computing a consensus of multilabeled trees. In ALENEX12, Pages 84-92, 2012. Keywords: duplication, explicit network, exponential algorithm, phylogenetic network, phylogeny. Note: http://siam.omnibooksonline.com/2012ALENEX/data/papers/020.pdf.         Toggle abstract In this paper we consider two challenging problems that arise in the context of computing a consensus of a collection of multilabeled trees, namely (1) selecting a compatible collection of clusters on a multiset from an ordered list of such clusters and (2) optimally refining high degree vertices in a multilabeled tree. Forming such a consensus is part of an approach to reconstruct the evolutionary history of a set of species for which events such as genome duplication and hybridization have occurred in the past. We present exact algorithms for solving (1) and (2) that have an exponential run-time in the worst case. To give some impression of their performance in practice, we apply them to simulated input and to a real biological data set highlighting the impact of several structural properties of the input on the performance. 36 Andreas W. M. Dress, Katharina Huber, Jacobus Koolen and Vincent Moulton. An Algorithm for Computing Virtual Cut Points in Finite Metric Spaces. In COCOA07, Vol. 4616:4-10 of LNCS, springer, 2007. Keywords: from distances. Note: http://dx.doi.org/10.1007/978-3-540-73556-4_3.         37 Andreas W. M. Dress, Katharina Huber and Vincent Moulton. Hereditarily Optimal Realizations: Why are they Relevant in Phylogenetic Analysis, and how does one Compute them? In Proceedings of the Euroconference on Algebraic Combinatorics and Applications (Alcoma'99), Pages 110-117, springer, 2001. Keywords: abstract network, from distances, optimal realization, phylogenetic network. Note: http://www.math.uni-bielefeld.de/fsp-math/Preprints/139.pdf.

InBook

38 Vincent Moulton and Katharina Huber. Split Networks. A tool for exploring complex evolutionary relationships in molecular data. In Philippe Lemey, Marco Salemi and Anne-Mieke Vandamme editors, The Phylogenetic Handbook, Cambridge University Press, 2009. Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.         39 Vincent Moulton and Katharina Huber. Phylogenetic Networks. In Olivier Gascuel editor, Mathematics of evolution and phylogeny, Pages 178-200, Oxford University Press, 2005.

Misc

40 Katharina Huber, Simone Linz and Vincent Moulton. Weakly displaying trees in temporal tree-child network. 2020. Keywords: cherry-picking, from rooted trees, phylogenetic network, phylogeny, reconstruction, rigidly displaying, time consistent network, tree-child network, weakly displaying. Note: https://arxiv.org/abs/2004.02634.         41 Katharina Huber, Leo van Iersel, Remie Janssen, Mark Jones, Vincent Moulton, Yukihiro Murakami and Charles Semple. Rooting for phylogenetic networks. 2019. Keywords: explicit network, from network, level k phylogenetic network, orchard network, orientation, phylogenetic network, phylogeny, reconstruction, stack-free network, tree-based network, tree-child network, valid network. Note: https://arxiv.org/abs/1906.07430.

Book

42 Andreas W. M. Dress, Katharina Huber, Jacobus Koolen, Andreas Spillner and Vincent Moulton. An Introduction to Phylogenetic Combinatorics. Cambridge University Press, 2012. Keywords: phylogenetic network, split network, survey. Note: http://www.amazon.fr/Basic-Phylogenetic-Combinatorics-Andreas-Dress/dp/0521768322.