Who is Who in Phylogenetic Networks

Publications related to 'characterization'   Order by:   Type | Year

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Associated keywords

abstract-network agreement-forest APX-hard characterization cherry-picking circular-split-system clustering distinguishability explicit-network flat FPT from-clusters from-distances from-network from-quartets from-rooted-trees from-sequences from-triplets FU-stable-network galled-tree hybridization identifiability integer-linear-programming level-k-phylogenetic-network NP-complete phylogenetic-network phylogeny planar polynomial population-genetics Program-Dendroscope pyramid reconstruction reticulation-visible-network semidirected-network split split-network stack-free-network statistical-model time-consistent-network tree-containment tree-based-network tree-child-network uniqueness unrooted-tree-based-network weak-hierarchy weakly-compatible

Article (Journal)

1 Arvind Gupta, Ján Manuch, Xiaohong Zhao and Ladislav Stacho. Characterization of the existence of galled-tree networks. In JBCB, Vol. 4(6):1309-1328, 2006. Keywords: characterization, galled tree. Note: http://www.pims.math.ca/~manuch/papers/characterization_JBCB2006.pdf.         2 Yun S. Song. A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree. In TCBB, Vol. 3(2):186-191, 2006. Keywords: characterization, from sequences, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction. Note: http://www.eecs.berkeley.edu/~yss/Pub/nasc4gall.pdf.         3 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.         4 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." 5 Ethan Cecchetti. Orientability of Phylogenetic Network Graphs. In Rose Hulman Undergraduate Math Journal, Vol. 8(2), 2007. Keywords: characterization, explicit network, phylogenetic network. Note: http://www.rose-hulman.edu/mathjournal/v8n2.php.         6 Peter J. Humphries, Simone Linz and Charles Semple. On the complexity of computing the temporal hybridization number for two phylogenies. In DAM, Vol. 161:871-880, 2013. Keywords: agreement forest, APX hard, characterization, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network. Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/TAFapx.pdf.         Toggle abstract "Phylogenetic networks are now frequently used to explain the evolutionary history of a set of species for which a collection of gene trees, reconstructed from genetic material of different parts of the species' genomes, reveal inconsistencies. However, in the context of hybridization, the reconstructed networks are often not temporal. If a hybridization network is temporal, then it satisfies the time constraint of instantaneously occurring hybridization events; i.e. all species that are involved in such an event coexist in time. Furthermore, although a collection of phylogenetic trees can often be merged into a hybridization network that is temporal, many algorithms do not necessarily find such a network since their primary optimization objective is to minimize the number of hybridization events. In this paper, we present a characterization for when two rooted binary phylogenetic trees admit a temporal hybridization network. Furthermore, we show that the underlying optimization problem is APX-hard and, therefore, NP-hard. Thus, unless P=NP, it is unlikely that there are efficient algorithms for either computing an exact solution or approximating it within a ratio arbitrarily close to one. © 2012 Elsevier B.V. All rights reserved." 7 Peter J. Humphries, Simone Linz and Charles Semple. Cherry picking: a characterization of the temporal hybridization number for a set of phylogenies. In BMB, Vol. 75(10):1879-1890, 2013. Keywords: characterization, cherry-picking, from rooted trees, hybridization, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network. Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/CPSpaper.pdf.         Toggle abstract "Recently, we have shown that calculating the minimum-temporal-hybridization number for a set P of rooted binary phylogenetic trees is NP-hard and have characterized this minimum number when P consists of exactly two trees. In this paper, we give the first characterization of the problem for P being arbitrarily large. The characterization is in terms of cherries and the existence of a particular type of sequence. Furthermore, in an online appendix to the paper, we show that this new characterization can be used to show that computing the minimum-temporal hybridization number for two trees is fixed-parameter tractable. © 2013 Society for Mathematical Biology." 8 Louxin Zhang. On Tree-Based Phylogenetic Networks. In JCB, Vol. 23(7):553-565, 2016. Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network. Note: http://arxiv.org/abs/1509.01663.         9 Monika Balvociute, David Bryant and Andreas Spillner. When can splits be drawn in the plane? In SIAM Journal on Discrete Mathematics, Vol. 31(2):839-856, 2017. Keywords: abstract network, characterization, flat, phylogenetic network, planar, split, split network. Note: http://arxiv.org/abs/1509.06104v1.         10 Laura Jetten and Leo van Iersel. Nonbinary tree-based phylogenetic networks. In TCBB, Vol. 15(1):205-217, 2018. Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network. Note: http://arxiv.org/abs/1601.04974.         11 Charles Semple. Phylogenetic Networks with Every Embedded Phylogenetic Tree a Base Tree. In BMB, Vol. 78(1):132-137, 2016. Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network, tree-child network. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S15.pdf.         12 Andrew R. Francis, Charles Semple and Mike Steel. New characterisations of tree-based networks and proximity measures. In Advances in Applied Mathematics, Vol. 93:93-107, 2018. Keywords: characterization, explicit network, phylogenetic network, phylogeny, time consistent network, tree-based network. Note: https://arxiv.org/abs/1611.04225.         13 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.         14 Joan Carles Pons, Charles Semple and Mike Steel. Tree-based networks: characterisations, metrics, and support trees. In JOMB, Vol. 78(4):899-918, 2019. Keywords: characterization, explicit network, from network, phylogenetic network, phylogeny, time consistent network, tree-based network. Note: https://arxiv.org/abs/1710.07836.         15 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.         16 Charles Semple and Jack Simpson. When is a phylogenetic network simply an amalgamation of two trees? In BMB, Vol. 80(9):2338-2348, 2018. Keywords: characterization, phylogenetic network, phylogeny, reticulation-visible network, stack-free network, tree-based network. Note: http://www.math.canterbury.ac.nz/~c.semple/papers/SS18.pdf.         17 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.         18 Michael Hendriksen. Tree-based unrooted nonbinary phylogenetic networks. In MBIO, Vol. 302:131-138, 2018. Keywords: characterization, phylogenetic network, phylogeny, tree-based network, unrooted tree-based network.

InProceedings

19 Hans-Jürgen Bandelt and Andreas W. M. Dress. A relational approach to split decomposition. In H.-H. Bock, W. Lenski and M. M. Richter editors, Information Systems and Data Analysis, Proceedings of the 17th Annual Conference of the Gesellschaft Für Klassifikation (GFKL93), Vol. 42:123-131 of Studies in Classification, Data Analysis, and Knowledge Organization, springer, 1994. Keywords: characterization, from quartets, phylogenetic network, weakly compatible.

PhdThesis

20 Philippe Gambette. Méthodes combinatoires de reconstruction de réseaux phylogénétiques. PhD thesis, Université Montpellier 2, France, 2010. Keywords: abstract network, characterization, circular split system, explicit network, FPT, from clusters, from triplets, integer linear programming, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, Program Dendroscope, pyramid, reconstruction, split network, weak hierarchy. Note: http://tel.archives-ouvertes.fr/tel-00608342/en/.

Misc

21 Dan Gusfield. On the Full-Decomposition Optimality Conjecture for Phylogenetic Networks. 2005. Keywords: characterization, explicit network, from sequences, phylogenetic network, reconstruction. Note: UC Davis Computer Science Technical Report CSE-2005, http://wwwcsif.cs.ucdavis.edu/~gusfield/fullydecomp.pdf.         22 Hans-Jürgen Bandelt. Four-point characterization of the dissimilarity functions obtained from indexed closed weak hierarchies. 1992. Keywords: characterization, clustering, from distances, pyramid, weak hierarchy. Note: Mathematisches Seminar, Universität Hamburg.         23 Laura Jetten. Characterising tree-based phylogenetic networks. Bachelor thesis, 2015. Keywords: characterization, explicit network, phylogenetic network, phylogeny, tree-based network. Note: http://resolver.tudelft.nl/uuid:fda2636d-0ed5-4dd2-bacf-8abbbad8994e.         24 Elizabeth Gross, Leo van Iersel, Remie Janssen, Mark Jones, Colby Long and Yukihiro Murakami. Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes. 2020. Keywords: characterization, distinguishability, explicit network, galled tree, phylogenetic network, population genetics, semidirected network, statistical model, uniqueness. Note: https://arxiv.org/abs/2007.08782.         25 Stefan Forcey and Drew Scalzo. Galois connections for phylogenetic networks and their polytopes. 2020. Keywords: characterization, from distances, galled tree, planar, reconstruction, split network. Note: https://arxiv.org/abs/2004.11944.