Publications related to 'from unrooted trees'
 
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2018
1
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Leo van Iersel, Steven Kelk, Giorgios Stamoulis, Leen Stougie and Olivier Boes. On unrooted and root-uncertain variants of several well-known phylogenetic network problems. In ALG, Vol. 80(11):2993-3022, 2018.
Keywords: explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment.
Note: https://hal.inria.fr/hal-01599716.
       

2
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Andrew R. Francis and Vincent Moulton. Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution. In JTB, Vol. 446:160-167, 2018.
Keywords: explicit network, from unrooted trees, phylogenetic network, phylogeny, tree-child network, uniqueness.
Note: https://arxiv.org/abs/1712.04223.
       

2017
3
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Klaus Schliep, Alastair J. Potts, David A. Morrison and Guido W. Grimm. Intertwining phylogenetic trees and networks. In Methods in Ecology and Evolution, Vol. 8(10):1212-1220, 2017.
Keywords: abstract network, from network, from unrooted trees, phylogenetic network, phylogeny, split network, visualization.
Note: http://dx.doi.org/10.1111/2041-210X.12760.
       

2016
4
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Claudia Solís-Lemus and Cécile Ané. Inferring phylogenetic networks with maximum pseudolikelihood under incomplete lineage sorting. In PLOS Genetics, Vol. 12(3):e1005896, 2016.
Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ.
Note: http://arxiv.org/abs/1509.06075v1.
       

2015
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Claudia Solís-Lemus. Statistical methods to infer population structure with coalescence and gene flow. PhD thesis, University of Wisconsin-Madison, 2015.
Keywords: explicit network, from quartets, from unrooted trees, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, semidirected network.
Note: https://www.stat.wisc.edu/~claudia/thesis.pdf.
       

2014
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Anthony Labarre and Sicco Verwer. Merging partially labelled trees: hardness and a declarative programming solution. In TCBB, Vol. 11(2):389-397, 2014.
Keywords: abstract network, from unrooted trees, heuristic, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-00855669.
       
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2013
7
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Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten and Ron Shamir. Systematic inference of highways of horizontal gene transfer in prokaryotes. In BIO, Vol. 29(5):571-579, 2013.
Keywords: duplication, explicit network, from species tree, from unrooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HiDe, Program RANGER-DTL, reconstruction.
Note: http://people.csail.mit.edu/mukul/Bansal_Highways_Bioinformatics_2013.pdf.
       

2012
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Hyun Jung Park and Luay Nakhleh. MURPAR: A fast heuristic for inferring parsimonious phylogenetic networks from multiple gene trees. In ISBRA12, Vol. 7292:213-224 of LNCS, springer, 2012.
Keywords: explicit network, from unrooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, software.
Note: https://www.researchgate.net/profile/Hyun_Jung_Park2/publication/262318595_MURPAR_A_Fast_Heuristic_for_Inferring_Parsimonious_Phylogenetic_Networks_from_Multiple_Gene_Trees/links/54b7e7b50cf269d8cbf58cc4.pdf.
       
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9
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Reza Hassanzadeh, Changiz Eslahchi and Wing-Kin Sung. Constructing phylogenetic supernetworks based on simulated annealing. In MPE, Vol. 63(3):738-744, 2012.
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.ympev.2012.02.009.
       
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2011
10
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Jean-Philippe 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 (RECOMB-CG'10), Vol. 6398:93-108 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/MPR-DoyonEtAl.pdf, software available at http://www.atgc-montpellier.fr/MPR/.
       
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11
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Changiz Eslahchi and Reza Hassanzadeh. New Algorithm for Constructing Supernetworks from Partial Trees. In MCCMB11, Pages 106-107, 2011.
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, split network.
Note: http://mccmb.belozersky.msu.ru/2011/mccmb11.pdf#page=106.
       

2009
12
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Josh Voorkamp né Collins. Rekernelisation Algorithms in Hybrid Phylogenies. Master's thesis, University of Canterbury, New Zealand, 2009.
Keywords: agreement forest, explicit network, FPT, from rooted trees, from unrooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://hdl.handle.net/10092/2852.
       

2008
13
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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/.
       
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14
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James B. Whitfield, Sydney A. Cameron, Daniel H. Huson and Mike Steel. Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees. In Systematic Biology, Vol. 57(6):939-947, 2008.
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, split, split network, supernetwork.
Note: http://www.life.uiuc.edu/scameron/pdfs/Filtered%20Z-closure%20SystBiol.pdf.
       

15
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Tobias Kloepper. Algorithms for the Calculation and Visualisation of Phylogenetic Networks. PhD thesis, Eberhard-Karls-Universität Tübingen, Germany, 2008.
Keywords: from rooted trees, from sequences, from unrooted trees, galled network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: https://publikationen.uni-tuebingen.de/xmlui/handle/10900/49159.
       

16
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Stefan Grünewald, Andreas Spillner, Kristoffer Forslund and Vincent Moulton. Constructing Phylogenetic Supernetworks from Quartets. In WABI08, Vol. 5251:284-295 of LNCS, springer, 2008.
Keywords: abstract network, from quartets, from unrooted trees, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_24.
       
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17
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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.
       
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18
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Anthony Labarre. Combinatorial aspects of genome rearrangements and haplotype networks. PhD thesis, Université Libre de Bruxelles, Belgium, 2008.
Keywords: abstract network, from unrooted trees, haplotype network, phylogenetic network, phylogeny, reconstruction.
Note: http://homepages.ulb.ac.be/~alabarre/publications/phd-thesis.pdf.
       

2007
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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.
       
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20
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Daniel H. Huson. Split networks and Reticulate Networks. In Olivier Gascuel and Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 247-276, Oxford University Press, 2007.
Keywords: abstract network, consensus, from rooted trees, from sequences, from splits, from unrooted trees, galled tree, hybridization, phylogenetic network, phylogeny, Program Beagle, Program Spectronet, Program SplitsTree, Program SPNet, recombination, reconstruction, split network, survey.
Note: similar to http://www-ab.informatik.uni-tuebingen.de/research/phylonets/GCB2006.pdf.
       

2006
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Robert G. Beiko and Nicholas Hamilton. Phylogenetic identification of lateral genetic transfer events. In BMCEB, Vol. 6(15), 2006.
Keywords: evaluation, from rooted trees, from unrooted trees, lateral gene transfer, Program EEEP, Program HorizStory, Program LatTrans, reconstruction, software, SPR distance.
Note: http://dx.doi.org/10.1186/1471-2148-6-15.
       
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2005
22
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Insa Cassens, Patrick Mardulyn and Michel C. Milinkovitch. Evaluating Intraspecific Network Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach? In Systematic Biology, Vol. 54(3):363-372, 2005.
Keywords: abstract network, evaluation, from unrooted trees, haplotype network, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program TCS, reconstruction, software.
Note: http://www.lanevol.org/LANE/publications_files/Cassens_etal_SystBio_2005.pdf.
       

2004
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Daniel H. Huson, Tobias Dezulian, Tobias Kloepper and Mike Steel. Phylogenetic Super-Networks from Partial Trees. In TCBB, Vol. 1(4):151-158, 2004.
Keywords: abstract network, from unrooted trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, supernetwork.
Note: http://hdl.handle.net/10092/3177.
       
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