Publications related to 'galled tree' : A galled tree is a phylogenetic network where reticulation cycles do not overlap. This can be seen as a blobbed tree where each blob is a cycle. Galled trees are also referred to as gt-networks, nested phylogenetic networks of nesting depth 1, level-1 phylogenetic networks. They are generalized by level-f phylogenetic networks, galled networks and tree-child phylogenetic networks.
 
Order by:   Type | Year
           related to:
Associated keywords
2020
1
photophoto
Gabriel Cardona and Louxin Zhang. Counting and Enumerating Tree-Child Networks and Their Subclasses. In JCSS, Vol. 114:84-104, 2020.
Keywords: counting, enumeration, explicit network, galled network, galled tree, normal network, phylogenetic network, phylogeny, tree-child network.
       

2
photo
Louxin Zhang. Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. In WALCOM20, Vol. 12049:22-27 of LNCS, Springer, 2020.
Keywords: cluster containment, galled network, galled tree, nearly-stable network, phylogenetic network, phylogeny, polynomial, reticulation-visible network, survey, time consistent network, tree containment, tree-based network, tree-child network.
       

3
photo
Marefatollah Mansouri. Combinatorial properties of phylogenetic networks. PhD thesis, Vienna University of Technology (Austria), Institute of Discrete Mathematics and Geometry, 2020.
Keywords: counting, explicit network, galled tree, level k phylogenetic network, normal network, phylogenetic network, phylogeny.
Note: https://dmg.tuwien.ac.at/bgitten/Theses/mansouri.pdf.
       

4
photophotophotophotophotophoto
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.
       

5
photophotophoto
Leo van Iersel, Vincent Moulton and Yukihiro Murakami. Reconstructibility of unrooted level-k phylogenetic networks from distances. In AAM, Vol. 120(102075):1-30, 2020.
Keywords: from distances, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://doi.org/10.1016/j.aam.2020.102075.
       

6

Cassandra Durell and Stefan Forcey. Level-1 phylogenetic networks and their balanced minimum evolution polytopes. In JOMB, Vol. 80:1235-1263, 2020.
Keywords: from distances, galled tree, phylogenetic network, phylogeny, reconstruction, split network.
Note: https://arxiv.org/pdf/1905.09160.pdf.
       

7

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.
       

2018
8
photophotophotophoto
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.
       

9
photo
Guillaume Scholz. New algorithms and mathematical tools for phylogenetics beyond trees. PhD thesis, University of East Anglia, 2018.
Keywords: circular split system, explicit network, explicit network, from splits, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction, split network, uniqueness.
Note: https://ueaeprints.uea.ac.uk/id/eprint/66952.
       

10
photophoto
Kuang-Yu Chang, Wing-Kai Hon and Sharma V. Thankachan. Compact Encoding for Galled-Trees and its Applications. In 2018 Data Compression Conference, Pages 297-306, 2018.
Keywords: compression, counting, explicit network, galled tree, phylogenetic network, polynomial.
       

2017
11
photophotophoto
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.
       

12
photophotophoto
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.
       

13
photophotophoto
Leo van Iersel, Vincent Moulton, Eveline De Swart and Taoyang Wu. Binets: fundamental building blocks for phylogenetic networks. In BMB, Vol. 79(5):1135-1154, 2017.
Keywords: approximation, explicit network, from binets, from subnetworks, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/s11538-017-0275-4.
       

2016
14
photophoto
Nikita Alexeev and Max A. Alekseyev. Combinatorial Scoring of Phylogenetic Networks. In COCOON16, Vol. 9797:560-572 of LNCS, Springer, 2016.
Keywords: cactus graph, counting, explicit network, galled tree, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1602.02841.
       

15
photophotophotophoto
James Oldman, Taoyang Wu, Leo van Iersel and Vincent Moulton. TriLoNet: Piecing together small networks to reconstruct reticulate evolutionary histories. In MBE, Vol. 33(8):2151-2162, 2016.
Keywords: explicit network, from subnetworks, from trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction.
       

16
photophoto
Ioannis G. Tollis and Konstantinos G. Kakoulis. Algorithms for Visualizing Phylogenetic Networks. In GD16, Vol. 9801:183-195 of LNCS, springer, 2016.
Keywords: explicit network, galled network, galled tree, NP complete, planar, visualization.
Note: http://arxiv.org/abs/1609.00755.
       

2015
17
photo
Dan Gusfield. Persistent Phylogeny: A Galled-Tree and Integer Linear Programming Approach. In BCB15, Pages 443-451, 2015.
Keywords: explicit network, from binary characters, galled tree, integer linear programming, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1506.00678.
       

18
photo
Maxime Morgado. Propriétés structurelles et relations des classes de réseaux phylogénétiques. Master's thesis, ENS Cachan, 2015.
Keywords: compressed network, distinct-cluster network, explicit network, galled network, galled tree, level k phylogenetic network, nested network, normal network, phylogenetic network, phylogeny, regular network, spread, tree containment, tree sibling network, tree-based network, tree-child network, unicyclic network.
       

2014
19
photophoto
Judith Keijsper and Rudi Pendavingh. Reconstructing a phylogenetic level-1 network from quartets. In BMB, Vol. 76(10):2517-2541, 2014.
Keywords: explicit network, from quartets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1308.5206.
       

2013
20
photo
Stephen J. Willson. Reconstruction of certain phylogenetic networks from their tree-average distances. In BMB, Vol. 75(10):1840-1878, 2013.
Keywords: explicit network, from distances, galled tree, normal network, phylogenetic network, phylogeny, unicyclic network.
Note: http://www.public.iastate.edu/~swillson/Tree-AverageReconPaper9.pdf.
       
Toggle abstract
2012
21
photophoto
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
22
photophoto
Jesper Jansson and Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In CPM12, Vol. 7354:385-398 of LNCS, springer, 2012.
Keywords: distance between networks, explicit network, from network, galled tree, phylogenetic network, phylogeny, polynomial, triplet distance.
Note: http://www.df.lth.se/~jj/Publications/d_rt_for_Galled_Trees5_CPM_2012.pdf.
       
Toggle abstract
2011
23
photophotophoto
Shlomo Moran, Sagi Snir and Wing-Kin Sung. Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower bounds. In ACM Transactions on Algorithms, Vol. 7(4), 2011.
Keywords: evaluation, galled tree, phylogenetic network.
Note: http://www.cs.technion.ac.il/~moran/r/PS/gnets-TOA-7Feb2007.pdf.
       
Toggle abstract
24
photophotophotophoto
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
25
photophoto
Leo van Iersel and Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ALG, Vol. 60(2):207-235, 2011.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic.
Note: http://dx.doi.org/10.1007/s00453-009-9333-0.
       
Toggle abstract
2010
26
photophotophotophoto
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
27
photophotophotophoto
Miguel Arenas, Mateus Patricio, David Posada and Gabriel Valiente. Characterization of Phylogenetic Networks with NetTest. In BMCB, Vol. 11:268, 2010.
Keywords: explicit network, galled tree, phylogenetic network, Program NetTest, software, time consistent network, tree sibling network, tree-child network, visualization.
Note: http://dx.doi.org/10.1186/1471-2105-11-268, software available at http://darwin.uvigo.es/software/nettest/.
       
Toggle abstract
2009
28
photophotophoto
Leo van Iersel, Steven Kelk and Matthias Mnich. Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks. In JBCB, Vol. 7(4):597-623, 2009.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://arxiv.org/pdf/0712.2932v2.
       

29
photo
Leo van Iersel. Algorithms, Haplotypes and Phylogenetic Networks. PhD thesis, Eindhoven University of Technology, The Netherlands, 2009.
Keywords: evaluation, explicit network, exponential algorithm, FPT, from triplets, galled tree, level k phylogenetic network, mu distance, phylogenetic network, phylogeny, polynomial, Program Level2, Program Marlon, Program Simplistic, Program T REX, reconstruction.
Note: http://www.win.tue.nl/~liersel/thesis_vaniersel_viewing.pdf.
       

30
photophotophoto
Philippe Gambette, Vincent Berry and Christophe Paul. The structure of level-k phylogenetic networks. In CPM09, Vol. 5577:289-300 of LNCS, springer, 2009.
Keywords: coalescent, explicit network, galled tree, level k phylogenetic network, phylogenetic network, Program Recodon.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00371485/en/.
       
Toggle abstract
31
photophoto
Francesc Rosselló and Gabriel Valiente. All that Glisters is not Galled. In MBIO, Vol. 221(1):54-59, 2009.
Keywords: galled tree, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/0904.2448.
       
Toggle abstract
32
photo
Gabriel Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R. Pages 184-208, Taylor & Francis/CRC Press, 2009.
Keywords: counting, distance between networks, galled tree, generation, phylogenetic network, phylogeny, survey, time consistent network, tree sibling network, tree-child network.
Note: http://books.google.fr/books?id=F4YIIUWb7yMC.
       

2008
33
photophoto
Leo van Iersel and Steven Kelk. Constructing the Simplest Possible Phylogenetic Network from Triplets. In ISAAC08, Vol. 5369:472-483 of LNCS, springer, 2008.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, Program Marlon, Program Simplistic.
Note: http://arxiv.org/abs/0805.1859.
       

34
photo
Wing-Kin Sung. Constructing a Galled Phylogenetic Network. In Ming-Yang Kao editor, Encyclopedia of Algorithms, Springer Reference, 2008.
Keywords: explicit network, from triplets, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/978-0-387-30162-4_92.
       

35
photophotophoto
Miguel Arenas, Gabriel Valiente and David Posada. Characterization of reticulate networks based on the coalescent with recombination. In MBE, Vol. 25(12):2517-2520, 2008.
Keywords: coalescent, evaluation, explicit network, galled tree, phylogenetic network, phylogeny, Program Recodon, regular network, simulation, tree sibling network, tree-child network.
Note: http://dx.doi.org/10.1093/molbev/msn219.
       
Toggle abstract
2007
36
photo
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.
       

37
photophotophotophoto
Dan Gusfield, Vikas Bansal, Vineet Bafna and Yun S. Song. A Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In JCB, Vol. 14(10):1247-1272, 2007.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, Program Beagle, Program GalledTree, recombination, reconstruction, software.
Note: http://www.eecs.berkeley.edu/~yss/Pub/decomposition.pdf.
       

2006
38
photophotophotophoto
Ho-Leung Chan, Jesper Jansson, Tak-Wah Lam and Siu-Ming Yiu. Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. In JBCB, Vol. 4(4):807-832, 2006.
Keywords: explicit network, from distances, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/dist_ugn7_JBCB2006.pdf.
       
Toggle abstract
39
photophoto
Jesper Jansson and Wing-Kin Sung. Inferring a level-1 phylogenetic network from a dense set of rooted triplets. In TCS, Vol. 363(1):60-68, 2006.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/ipnrt8_TCS2006.pdf.
       
Toggle abstract
40
photophotophoto
Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SICOMP, Vol. 35(5):1098-1121, 2006.
Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/triplets_to_gn7_SICOMP2006.pdf.
       
Toggle abstract
41
photophoto
Charles Semple and Mike Steel. Unicyclic networks: compatibility and enumeration. In TCBB, Vol. 3(1):84-91, 2006.
Keywords: counting, explicit network, galled tree, unicyclic network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/SS06.pdf.
       

42
photophotophotophoto
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.
       

43
photo
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.
       

44
photophoto
Guillaume Bourque and Louxin Zhang. Models and Methods in Comparative Genomics. In Chau-Wen Tseng editor, Advances in Computers, Special Volume: Computational Biology, Vol. 68, Elsevier, 2006.
Keywords: from distances, from rooted trees, from sequences, galled tree, phylogenetic network, phylogeny, survey.
Note: http://www.math.nus.edu.sg/~matzlx/papers/CompGen_ZLX.pdf.
       

2005
45
photophotophotophoto
Ho-Leung Chan, Jesper Jansson, Tak-Wah Lam and Siu-Ming Yiu. Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. In MFCS05, Vol. 3618:224-235 of LNCS, springer, 2005.
Keywords: from distances, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/11549345_20.
       

46
photo
Elena Dubrova. Phylogenetic networks with edge-disjoint recombination cycles. In Proceedings of SPIE Bioengineered and Bioinspired Systems II (SPIE-BBS II), Vol. 5839:381-388, 2005.
Keywords: galled tree, phylogenetic network, polynomial, site consistency.
Note: http://dx.doi.org/10.1117/12.607910.
       
Toggle abstract
47
photophotophotophoto
Trinh N. D. Huynh, Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Constructing a Smallest Refining Galled Phylogenetic Network. In RECOMB05, Vol. 3500:265-280 of LNCS, springer, 2005.
Keywords: from rooted trees, galled tree, NP complete, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/refining_gn3_RECOMB2005.pdf.
       

48
photophotophoto
Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. In SODA05, Pages 349-358, 2005.
Keywords: approximation, explicit network, from triplets, galled tree, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://portal.acm.org/citation.cfm?id=1070481.
       

49
photophotophotophoto
Luay Nakhleh, Tandy Warnow, C. Randal Linder and Katherine St. John. Reconstructing reticulate evolution in species - theory and practice. In JCB, Vol. 12(6):796-811, 2005.
Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NWLSjcb.pdf.
       

2004
50
photophotophoto
Dan Gusfield, Satish Eddhu and Charles Langley. Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination. In JBCB, Vol. 2(1):173-213, 2004.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/exfinalrec.pdf.
       
Toggle abstract
51
photophotophoto
Dan Gusfield, Satish Eddhu and Charles Langley. The fine structure of galls in phylogenetic networks. In INCOMP, Vol. 16(4):459-469, 2004.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/informs.pdf.
       
Toggle abstract
52
photophoto
Jesper Jansson and Wing-Kin Sung. Inferring a level-1 phylogenetic network from a dense set of rooted triplets. In COCOON04, Vol. 3106:462-471 of LNCS, springer, 2004.
Keywords: explicit network, from triplets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/ipnrt6_COCOON2004.pdf.
       

53
photophotophoto
Luay Nakhleh, Tandy Warnow and C. Randal Linder. Reconstructing reticulate evolution in species - theory and practice. In RECOMB04, Pages 337-346, 2004.
Keywords: from rooted trees, galled tree, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction, software.
Note: http://www.cs.rice.edu/~nakhleh/Papers/144-nakhleh.pdf.
       

54
photo
Mihaela Baroni. Hybrid phylogenies : a graph-based approach to represent reticulate evolution. PhD thesis, University of Canterbury, New Zealand, 2004.
Keywords: explicit network, from rooted trees, galled tree, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, regular network.
Note: http://ir.canterbury.ac.nz/bitstream/10092/4803/1/baroni_thesis.pdf.
       

2003
55
photophotophoto
Dan Gusfield, Satish Eddhu and Charles Langley. Efficient reconstruction of phylogenetic networks with constrained recombination. In CSB03, Pages 363-374, 2003.
Keywords: explicit network, from sequences, galled tree, phylogenetic network, phylogeny, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/ieeefinal.pdf.
       

2001
56
photophotophoto
Lusheng Wang, Kaizhong Zhang and Louxin Zhang. Perfect phylogenetic networks with recombination. In SAC01, Pages 46-50, 2001.
Keywords: from sequences, galled tree, NP complete, perfect, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://dx.doi.org/10.1145/372202.372271.
       

2000
57
photophotophoto
Bin Ma, Lusheng Wang and Ming Li. Fixed topology alignment with recombination. In DAM, Vol. 104:281-300, 2000.
Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.40.7759.
       
Toggle abstract
1998
58
photophotophoto
Bin Ma, Lusheng Wang and Ming Li. Fixed topology alignment with recombination. In CPM98, Vol. 1448:174-188 of LNCS, springer, 1998.
Keywords: approximation, explicit network, from network, from sequences, galled tree, inapproximability, phylogenetic network, phylogeny, recombination.
Note: http://dx.doi.org/10.1007/BFb0030789.