Search results for ' BIO ' :
    574 matches found.
1
photophoto
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
photophotophoto
Andrew R. Francis, Daniel H. Huson and Mike Steel. Normalising phylogenetic networks. 2020.
Keywords: explicit network, from network, normal network, phylogenetic network, phylogeny, polynomial, Program PhyloSketch, reconstruction, tree-child network.
Note: https://arxiv.org/abs/2008.07797.
       

3
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.
       

4
photophoto
Michael Fuchs, Guan-Ru Yu and Louxin Zhang. On the Asymptotic Growth of the Number of Tree-Child Networks. 2020.
Keywords: counting, explicit network, phylogenetic network, phylogeny, tree-child network.
Note: https://arxiv.org/abs/2003.08049.
       

5
photophoto
Andreas Gunawan, Jeyaram Rathin and Louxin Zhang. Counting and enumerating galled networks. In DAM, Vol. 283:644-654, 2020.
Keywords: counting, enumeration, explicit network, galled network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1812.08569.
       

6
photo
Marefatollah Mansouri. Counting General Phylogenetic networks. 2020.
Keywords: counting, explicit network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/2005.14547.
       

7
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.
       

8
photophoto
Mathilde Bouvel, Philippe Gambette and Marefatollah Mansouri. Counting Phylogenetic Networks of Level 1 and 2. In JOMB, 2020.
Keywords: counting, explicit network, level k phylogenetic network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1909.10460, to appear.
       

9
photo
Jonathan Klawitter and Peter Stumpf. Drawing Tree-Based Phylogenetic Networks with Minimum Number of Crossings. 2020.
Keywords: explicit network, FPT, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, visualization.
Note: https://arxiv.org/abs/2008.08960.
       

10
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.
       

11
photophotophoto
Remie Janssen, Mark Jones and Yukihiro Murakami. Combining Networks Using Cherry Picking Sequences. In AlCoB20, Vol. 12099:77-92 of LNCS, Springer, 2020.
Keywords: cherry-picking, explicit network, FPT, from network, hybridization, orchard network, phylogenetic network, phylogeny, tree-child network.
       

12
photo
Hannah Brown, Lei Zuo and Dan Gusfield. Comparing Integer Linear Programming to SAT-Solving for Hard Problems in Computational and Systems Biology. In AlCoB2020, Vol. 12099:63-76 of LNCS, Springer, 2020.
Keywords: from binary characters, History bound, integer linear programming, minimum number, phylogeny, SAT.
Note: https://doi.org/10.1007/978-3-030-42266-0_6.
       

13
photophoto
Remie Janssen and Yukihiro Murakami. Linear Time Algorithm for Tree-Child Network Containment. In AlCoB20, Vol. 12099:93-107 of LNCS, Springer, 2020.
Keywords: explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, tree-child sequence.
Note: https://doi.org/10.1007/978-3-030-42266-0_8.
       

14
photo
Jonathan Klawitter. The agreement distance of unrooted phylogenetic networks. In DMTCS, Vol. 21(2):22.1-23, 2020.
Keywords: agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny.
Note: https://dmtcs.episciences.org/6567/pdf.
       

15
photophoto
Simone Linz and Charles Semple. Caterpillars on three and four leaves are sufficient to reconstruct binary normal networks. In JOMB, 2020.
Keywords: explicit network, from rooted trees, from triplets, normal network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://arxiv.org/abs/2002.00483, to appear.
       

16
photophoto
Hadi Poormohammadi and Mohsen Sardari Zarchi. Netcombin: An algorithm for constructing optimal phylogenetic network from rooted triplets. In PLoS ONE, Vol. 15(9):e0227842.1-25, 2020.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction.
Note: https://doi.org/10.1371/journal.pone.0227842.
       

17
photophoto
Hadi Poormohammadi, Mohsen Sardari Zarchi and Hossein Ghaneai. NCHB: A method for constructing rooted phylogenetic networks from rooted triplets based on height function and binarization. In JTB, Vol. 489(110144), 2020.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, Program Simplistic, Program TripNet, reconstruction.
Note: https://doi.org/10.1016/j.jtbi.2019.110144.
       

18
photophotophoto
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.
       

19
photophotophoto
Joan Carles Pons, Celine Scornavacca and Gabriel Cardona. Generation of Level-k LGT Networks. In TCBB, Vol. 17(1):158-164, 2020.
Keywords: explicit network, level k phylogenetic network, LGT network, phylogenetic network, phylogeny.
       

20
photophotophotophoto
Steven Kelk, Fabio Pardi, Celine Scornavacca and Leo van Iersel. Finding the most parsimonious or likely tree in a network with respect to an alignment. In JOMB, Vol. 78:527-547, 2019.
Keywords: APX hard, from network, from sequences, likelihood, NP complete, parsimony.
Note: https://arxiv.org/abs/1707.03648.
       

21
photophotophoto
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.
       

22
photophotophoto
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.
       

23
photophoto
Simone Linz and Charles Semple. Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies. In AAM, Vol. 105:102-129, 2019.
Keywords: agreement forest, cherry-picking, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: https://doi.org/10.1016/j.aam.2019.01.004.
       

24
photo
Jonathan Klawitter. The agreement distance of rooted phylogenetic networks. In DMTCS, Vol. 21(3):19.1-24, 2019.
Keywords: agreement forest, distance between networks, explicit network, from network, phylogenetic network, phylogeny, SPR distance.
Note: https://arxiv.org/abs/1806.05800.
       

25
photophotophotophoto
Janosch Döcker, Leo van Iersel, Steven Kelk and Simone Linz. Deciding the existence of a cherry-picking sequence is hard on two trees. In DAM, Vol. 260:131-143, 2019.
Keywords: cherry-picking, explicit network, hybridization, minimum number, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.02965.
       

26
photophoto
Jonathan Klawitter and Simone Linz. On the Subnet Prune and Regraft Distance. In ELJC, Vol. 26(2):P2.3.1-23, 2019.
Keywords: agreement forest, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://arxiv.org/abs/1805.07839.
       

27
photophotophoto
Michael Fuchs, Bernhard Gittenberger and Marefatollah Mansouri. Counting Phylogenetic Networks with Few Reticulation Vertices: Tree-Child and Normal Networks. In Australasian Journal of Combinatorics, Vol. 73(2):385-423, 2019.
Keywords: counting, explicit network, normal network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1803.11325, see also erratum at https://arxiv.org/abs/2006.15784.
       

28
photophoto
Andreas Gunawan, Hongwei Yan and Louxin Zhang. Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem. In JCB, Vol. 25(3), 2019.
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, quasi-reticulation-visible network, reticulation-visible network, tree containment, tree-child network.
Note: https://arxiv.org/abs/1806.07625.
       

29
photophoto
R. A. Leo Elworth, Huw A. Ogilvie, Jiafan Zhu and Luay Nakhleh. Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization. In Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29 of Computational Biology, Springer, 2019.
Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program PhyloNet, Program PhyloNetworks SNaQ, Program PIRN, Program SplitsTree, reconstruction, survey.
Note: https://bioinfocs.rice.edu/sites/g/files/bxs266/f/ElworthZhuOgilvieNakhleh.pdf
       

30
photo
Louxin Zhang. Clusters, Trees, and Phylogenetic Network Classes. In Tandy Warnow editor, Bioinformatics and Phylogenetics. Seminal Contributions of Bernard Moret, Vol. 29:277-315 of Computational Biology, Springer, 2019.
Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, polynomial, tree containment.
       

31
photo
Louxin Zhang. Generating normal networks via leaf insertion and nearest neighbor interchange. In BMC Bioinformatics, Vol. 20(642):1-9, 2019.
Keywords: enumeration, explicit network, generation, NNI moves, phylogenetic network, phylogeny.
Note: https://link.springer.com/content/pdf/10.1186/s12859-019-3209-3.pdf.
       

32
photophoto
Juan Wang and Maozu Guo. IGNet: Constructing Rooted Phylogenetic Networks Based on Incompatible Graphs. In ICNC-FSKD19, Vol. 1075:894-900 of Advances in Intelligent Systems and Computing, Springer, 2019.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program IGNet, Program LNetwork, reconstruction, software.
       

33
photo
Yan Hong and Juan Wang. Frin: An Efficient Method for Representing Genome Evolutionary History. In Frontiers in Genetics, Vol. 10(1261):1-8, 2019.
Keywords: explicit network, from clusters, phylogenetic network, phylogeny, Program Frin, reconstruction.
Note: https://doi.org/10.3389/fgene.2019.01261.
       

34
photophoto
Juan Wang and Maozu Guo. A review of metrics measuring dissimilarity for rooted phylogenetic networks. In Briefings in Bioinformatics, Vol. 20(6):1972-1980, 2019.
Keywords: distance between networks, explicit network, from network, mu distance, phylogenetic network, phylogeny, survey, tree sibling network, tree-child network.
       

35
photo
Christopher Blair and Cécile Ané. Phylogenetic trees and networks can serve as powerful and complementary approaches for analysis of genomic data. In SB, Vol. 69(3):593-601, 2019.
Keywords: likelihood, phylogenetic network, phylogeny, Program PhyloNetwork, Program PhyloNetworks SNaQ, survey.
       

36

Konstantinos Mampentzidis. Comparison and Construction of Phylogenetic Trees and Networks. PhD thesis, Aarhus University, Denmark, 2019.
Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, triplet distance.
Note: https://pure.au.dk/ws/files/172250681/thesis_Konstantinos_Mampentzidis.pdf.
       

37
photophotophoto
Janosch Döcker, Simone Linz and Charles Semple. Displaying trees across two phylogenetic networks. In TCS, Vol. 796:129-146, 2019.
Keywords: display set, explicit network, normal network, phylogenetic network, phylogeny, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1901.06612.
       

38
photophotophotophotophotophotophoto
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.
       

39
photophotophoto
Gabriel Cardona, Joan Carles Pons and Celine Scornavacca. Generation of Binary Tree-Child phylogenetic networks. In PLoS Computational Biology, Vol. 15(10):e1007440.1-29, 2019.
Keywords: enumeration, explicit network, generation, phylogenetic network, phylogeny, Program PhyloNetwork, Program TCGenerators, software, tree-child network.
Note: https://doi.org/10.1371/journal.pcbi.1007440.
       

40
photophotophotophoto
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.
       

41
photophoto
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.
       

42
photophoto
Daniel H. Huson and Simone Linz. Autumn Algorithm - Computation of Hybridization Networks for Realistic Phylogenetic Trees. In TCBB, Vol. 15:398-410, 2018.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, reconstruction.
Note: https://simonelinz.files.wordpress.com/2016/06/hl16.pdf.
       

43
photophotophoto
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.
       

44
photo
Mathias Weller. Linear-Time Tree Containment in Phylogenetic Networks. In RECOMB-CG18, Vol. 11183:309-323 of LNCS, Springer, 2018.
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, reconstruction, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.06364.
       

45
photophotophotophoto
Hussein A. Hejase, Natalie VandePol, Gregory A. Bonito and Kevin J. Liu. Fast and accurate statistical inference of phylogenetic networks using large-scale genomic sequence data. In RECOMB-CG18, Vol. 11183:242-259 of LNCS, Springer, 2018.
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: http://biorxiv.org/content/early/2017/05/01/132795.
       

46
photophotophoto
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.
       

47
photophotophoto
Magnus Bordewich, Charles Semple and Nihan Tokac. Constructing tree-child networks from distance matrices. In Algorithmica, Vol. 80(8):2240-2259, 2018.
Keywords: compressed network, explicit network, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, tree-child network, uniqueness.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSN17.pdf.
       

48
photo
Andreas Gunawan. Solving the Tree Containment Problem for Reticulation-visible Networks in Linear Time. In AlCoB18, Vol. 10849:24-36 of LNCS, Springer, 2018.
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.04088.
       

49
photophotophotophotophoto
Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem in Linear Time for Nearly Stable Phylogenetic Networks. In DAM, Vol. 246:62-79, 2018.
Keywords: explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01575001/en/.
       

50
photophotophotophotophoto
Remie Janssen, Mark Jones, Péter L. Erdös, Leo van Iersel and Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves. In BMB, Vol. 80(8):2177-2208, 2018.
Keywords: distance between networks, explicit network, from network, NNI moves, orientation, phylogenetic network, phylogeny, SPR distance.
Note: https://arxiv.org/abs/1708.07656.
       

51
photophotophotophotophotophoto
Sarah Bastkowski, Daniel Mapleson, Andreas Spillner, Taoyang Wu, Monika Balvociute and Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. In BIO, Vol. 34(6):1057-1058, 2018.
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: https://doi.org/10.1101/169177.
       

52
photophoto
Sebastien Roch and Kun-Chieh Wang. Circular Networks from Distorted Metrics. In RECOMB18, Vol. 10812:167-176 of LNCS, Springer, 2018.
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network.
Note: https://arxiv.org/abs/1707.05722.
       

53
photophotophoto
Paul Bastide, Claudia Solís-Lemus, Ricardo Kriebel, Kenneth William Sparks and Cécile Ané. Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations. In SB, Vol. 67(5):800-820, 2018.
Keywords: ancestral trait reconstruction, from network, likelihood, Program PhyloNetworks SNaQ, software, statistical model, statistical test.
Note: https://doi.org/10.1101/194050.
       

54
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.
       

55
photophoto
Leo van Iersel and Vincent Moulton. Leaf-reconstructibility of phylogenetic networks. In SIAM Journal on Discrete Mathematics, Vol. 32(3):2047-2066, 2018.
Keywords: explicit network, from network, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://arxiv.org/abs/1701.08982.
       

56
photophoto
Kristina Wicke and Mareike Fischer. Phylogenetic diversity and biodiversity indices on phylogenetic networks. In MB, Vol. 298:80-90, 2018.
Keywords: diversity, explicit network, from network, normal network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1706.05279.
       

57
photophoto
Magnus Bordewich and Charles Semple. A universal tree-based network with the minimum number of reticulations. In DAM, Vol. 250:357-362, 2018.
Keywords: explicit network, phylogenetic network, phylogeny, tree-based network.
Note: https://arxiv.org/abs/1707.08274.
       

58
photophoto
Janosch Döcker and Simone Linz. On the existence of a cherry-picking sequence. In TCS, Vol. 714:36-50, 2018.
Keywords: cherry-picking, explicit network, from rooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, temporal-hybridization number, time consistent network, tree-child network.
Note: https://arxiv.org/abs/1712.04127.
       

59
photo
James H. Degnan. Modeling Hybridization Under the Network Multispecies Coalescent. In SB, Vol. 67(5):786-799, 2018.
Keywords: distance between networks, phylogenetic network, phylogeny, reconstruction, survey.
Note: https://academic.oup.com/sysbio/article/67/5/786/5017269.
       

60
photophoto
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.
       

61
photophotophoto
Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, Vol. 67(3):518-542, 2018.
Keywords: explicit network, FPT, from sequences, NP complete, parsimony, phylogenetic network, phylogeny, reconstruction, weakly displaying.
Note: https://leovaniersel.files.wordpress.com/2017/12/improved_parsimony_networks.pdf.
       

62
photo
Sajad Mirzaei. Efficient Algorithms for Trees and Networks in Evolutionary Genomics. PhD thesis, University of Connecticut, 2018.
Keywords: branch length, explicit network, haplotype network, heuristic, Program PIRN, reconstruction.
Note: https://opencommons.uconn.edu/dissertations/1853.
       

63
photophotophotophoto
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.
       

64
photophotophotophoto
Chi Zhang, Huw A. Ogilvie, Alexei J. Drummond and Tanja Stadler. Bayesian Inference of Species Networks from Multilocus Sequence Data. In MBE, Vol. 35(2):504-517, 2018.
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: https://dx.doi.org/10.1093/molbev/msx307.
       

65
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.
       

66
photophotophoto
Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In JCB, Vol. 25(3):253-269, 2018.
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.
       

67
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.
       

68
photophoto
Hongwei Yan, Andreas Gunawan and Louxin Zhang. S-Cluster++: a fast program for solving the cluster containment problem for phylogenetic networks. In BIO, Vol. 34(17):i680–i686, 2018.
Keywords: cluster containment, explicit network, phylogenetic network, phylogeny, SAT.
Note: http://dx.doi.org/10.1093/bioinformatics/bty594.
       

69

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.
       

70
photophotophoto
Dingqiao Wen, Yun Yu, Jiafan Zhu and Luay Nakhleh. Inferring Phylogenetic Networks Using PhyloNet. In SB, Vol. 67(4):735-740, 2018.
Keywords: bayesian, likelihood, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
       

71
photophotophoto
Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt and Luay Nakhleh. Bayesian inference of phylogenetic networks from bi-allelic genetic markers. In PLoS Computational Biology, Vol. 14(1):e1005932.1-32, 2018.
Keywords: bayesian, explicit network, from multistate characters, phylogenetic network, phylogeny, Program PhyloNet.
Note: https://doi.org/10.1371/journal.pcbi.1005932.
       

72
photophoto
Dingqiao Wen and Luay Nakhleh. Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data. In SB, Vol. 67(3):439-457, 2018.
Keywords: bayesian, explicit network, from sequences, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://doi.org/10.1093/sysbio/syx085.
       

73
photo
Andreas Gunawan. On the tree and cluster containment problems for phylogenetic networks. PhD thesis, National University of Singapore, 2018.
Keywords: cluster containment, explicit network, galled network, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, tree containment.
Note: https://scholarbank.nus.edu.sg/handle/10635/144270.
       

74
photophotophotophotophoto
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.
       

75
photophotophotophoto
Christopher Bryant, Mareike Fischer, Simone Linz and Charles Semple. On the Quirks of Maximum Parsimony and Likelihood on Phylogenetic Networks. In JTB, Vol. 417:100-108, 2017.
Keywords: explicit network, from sequences, likelihood, parsimony, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1505.06898.
       

76
photophotophoto
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.
       

77
photophoto
Satyan L. Devadoss and Samantha Petti. A Space of Phylogenetic Networks. In SIAM Journal on Applied Algebra and Geometry, Vol. 1(1):683-705, 2017.
Keywords: abstract network, circular split system, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/1607.06978.
       

78
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.
       

79
photophotophotophotophoto
Julia Matsieva, Steven Kelk, Celine Scornavacca, Chris Whidden and Dan Gusfield. A Resolution of the Static Formulation Question for the Problem of Computing the History Bound. In TCBB, Vol. 14(2):404-417, 2017.
Keywords: ARG, explicit network, from sequences, minimum number, phylogenetic network, phylogeny.
       

80
photophoto
Sha Zhu and James H. Degnan. Displayed Trees Do Not Determine Distinguishability Under the Network Multispecies Coalescent. In SB, Vol. 66(2):283-298, 2017.
Keywords: branch length, coalescent, explicit network, from network, likelihood, phylogenetic network, phylogeny, Program Hybrid-coal, Program Hybrid-Lambda, Program PhyloNet, software, uniqueness.
Note: presentation available at https://www.youtube.com/watch?v=JLYGTfEZG7g.
       

81
photophoto
Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In TCBB, Vol. 14(3):587-599, 2017.
Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://compbio.engr.uconn.edu/papers/Kordi_DTLreconciliationPreprint2015.pdf.
       

82
photophotophoto
Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. A decomposition theorem and two algorithms for reticulation-visible networks. In Information and Computation, Vol. 252:161-175, 2017.
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://www.cs.uic.edu/~dasgupta/resume/publ/papers/Infor_Comput_IC4848_final.pdf.
       

83
photophoto
Gabriel Cardona and Joan Carles Pons. Reconstruction of LGT networks from tri-LGT-nets. In JOMB, Vol. 75(6-7):1669-1692, 2017.
Keywords: explicit network, from subnetworks, from tri-LGT-nets, LGT network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://doi.org/10.1007/s00285-017-1171-0.
       

84
photophotophoto
Bingxin Lu, Louxin Zhang and Hon Wai Leong. A program to compute the soft Robinson-Foulds distance between phylogenetic networks. In APBC17, Vol. 18(Suppl. 2):111 of BMC Genomics, 2017.
Keywords: cluster containment, distance between networks, explicit network, exponential algorithm, from network, phylogenetic network, phylogeny, Program icelu-PhyloNetwork.
Note: http://dx.doi.org/10.1186/s12864-017-3500-5.
       

85
photophotophoto
Vincent Moulton, James Oldman and Taoyang Wu. A cubic-time algorithm for computing the trinet distance between level-1 networks. In IPL, Vol. 123:36-41, 2017.
Keywords: distance between networks, explicit network, from network, phylogenetic network, phylogeny, polynomial, Program TriLoNet.
Note: https://doi.org/10.1016/j.ipl.2017.03.002.
       

86
photophoto
Olga K. Kamneva and Noah A. Rosenberg. Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting. In Evolutionary Bioinformatics, Vol. 13(1176934317691935):1-16, 2017.
Keywords: evaluation, explicit network, incomplete lineage sorting, simulation.
Note: https://dx.doi.org/10.1177%2F1176934317691935.
       

87
photophotophoto
Magnus Bordewich, Simone Linz and Charles Semple. Lost in space? Generalising subtree prune and regraft to spaces of phylogenetic networks. In JTB, Vol. 423:1-12, 2017.
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, reticulation-visible network, SPR distance, tree-based network, tree-child network.
Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.
       

88
photophotophoto
Celine Scornavacca, Joan Carles Pons and Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. In JTB, Vol. 418:129-137, 2017.
Keywords: duplication, explicit network, from network, from rooted trees, lateral gene transfer, LGT network, loss, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
       

89
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.
       

90
photophoto
Juan Wang and Maozu Guo. A Metric on the Space of kth-order reduced Phylogenetic Networks. In Scientific Reports, Vol. 7(3189):1-10, 2017.
Keywords: distance between networks, explicit network, from network, kth-order reduced network, phylogenetic network, phylogeny, polynomial.
Note: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466651/.
       

91
photophotophotophotophotophoto
Philippe Gambette, Leo van Iersel, Mark Jones, Manuel Lafond, Fabio Pardi and Celine Scornavacca. Rearrangement Moves on Rooted Phylogenetic Networks. In PLoS Computational Biology, Vol. 13(8):e1005611.1-21, 2017.
Keywords: distance between networks, explicit network, from network, NNI distance, NNI moves, phylogenetic network, phylogeny, SPR distance.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/.
       

92
photophotophoto
Han Lai, Maureen Stolzer and Dannie Durand. Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses. In RECOMB-CG17, Vol. 10562:298-320 of LNCS, Springer, 2017.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.
       

93
photophotophotophoto
Ruzbeh Tusserkani, Hadi Poormohammadi, Azin Azadi and Changiz Eslahchi. Inferring phylogenies from minimal information. In AEEICB17, Pages 202-206, IEEE, 2017.
Keywords: from triplets, phylogenetic network, phylogeny, Program TripNet, reconstruction.
       

94
photophotophotophoto
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.
       

95

Timothy G. Vaughan. IcyTree: rapid browser-based visualization for phylogenetic trees and networks. In BIO, Vol. 33(15):2392-2394, 2017.
Keywords: ARG, explicit network, from network, phylogenetic network, phylogeny, Program IcyTree, software, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btx155.
       

96
photo
Mohammad Hossein Reyhani and Hadi Poormohammadi. RPNCH: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets based on Height Function. In Archives of Advances in Biosciences, Vol. 8(4):14-20, 2017.
Keywords: explicit network, from triplets, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://journals.sbmu.ac.ir/jps/article/view/16707.
       

97
photo
Hussein A. Hejase. Scalable Phylogenetic Analysis and Functional Interpretation of Genomes with Complex Evolutionary Histories. PhD thesis, Michigan State University, 2017.
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: https://dx.doi.org/10.25335/M5T855.
       

98
photophotophotophoto
Edwin Jacox, Mathias Weller, Eric Tannier and Celine Scornavacca. Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses. In BIO, Vol. 33(7):980-987, 2017.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btw778.
       

99
photo
Luay Nakhleh. Phylogenetic Networks: From Displayed Trees to a Distribution of Gene Trees. Phyloseminar #70, 2017.
Keywords: bayesian, coalescent, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, statistical model.
Note: https://www.youtube.com/watch?v=dkQsvLUUDcQ.
       

100
photo
Celine Scornavacca. Occam's razor in phylogenetic network reconstruction. Phyloseminar #71, 2017.
Keywords: explicit network, from rooted trees, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: https://www.youtube.com/watch?v=W6tEVulgQu8.
       

101
photo
Cécile Ané. From reconstructing to using phylogenetic networks. Phyloseminar #72, 2017.
Keywords: explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, semidirected network.
Note: https://www.youtube.com/watch?v=PF4j_JOQP0c.
       

102
photo
Paul Bastide. Shifted stochastic processes evolving on trees : application to models of adaptive evolution on phylogenies. PhD thesis, Université Paris Saclay, 2017.
Keywords: ancestral trait reconstruction, bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNetworks SNaQ, reconstruction, statistical model.
Note: https://tel.archives-ouvertes.fr/tel-01629648/en/, slides..
       

103
photophotophoto
Kuang-Yu Chang, Yun Cui, Siu-Ming Yiu and Wing-Kai Hon. Reconstructing One-Articulated Networks with Distance Matrices. In ISBRA17, Vol. 10330:34-45 of LNCS, Springer, 2017.
Keywords: explicit network, from distances, k-reticulated, phylogenetic network, phylogeny, reconstruction.
Note: https://link.springer.com/content/pdf/10.1007%2F978-3-319-59575-7.pdf#page=100.
       

104
photo
Dingqiao Wen. Bayesian Inference of Phylogenetic Networks from Sequence Data. PhD thesis, Rice University, 2017.
Keywords: bayesian, explicit network, phylogenetic network, phylogeny, reconstruction.
       

105
photophotophotophotophoto
Leo van Iersel, Steven Kelk, Nela Lekic, Chris Whidden and Norbert Zeh. Hybridization Number on Three Rooted Binary Trees is EPT. In SIDMA, Vol. 30(3):1607-1631, 2016.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1402.2136.
       

106
photophotophotophoto
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.
       

107
photophotophotophoto
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.
       

108
photophotophotophoto
Steven Kelk, Leo van Iersel, Celine Scornavacca and Mathias Weller. Phylogenetic incongruence through the lens of Monadic Second Order logic. In JGAA, Vol. 20(2):189-215, 2016.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, MSOL, phylogenetic network, phylogeny, reconstruction.
Note: http://jgaa.info/accepted/2016/KelkIerselScornavaccaWeller2016.20.2.pdf.
       

109
photo
Stephen J. Willson. Comparing and simplifying distinct-cluster phylogenetic networks. In ACOM, Vol. 20(4):917-938, 2016.
Keywords: distinct-cluster network, explicit network, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1501.07528.
       

110
photophotophoto
Andreas Gunawan, Bhaskar DasGupta and Louxin Zhang. Locating a Tree in a Reticulation-Visible Network in Cubic Time. In RECOMB16, Vol. 9649:266 of LNBI, Springer, 2016.
Keywords: cluster containment, explicit network, from clusters, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: http://arxiv.org/abs/1507.02119.
       

111
photophoto
Sajad Mirzaei and Yufeng Wu. Fast Construction of Near Parsimonious Hybridization Networks for Multiple Phylogenetic Trees. In TCBB, Vol. 13(3):565-570, 2016.
Keywords: bound, explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PIRN, reconstruction, software.
Note: http://www.engr.uconn.edu/~ywu/Papers/PIRNs-preprint.pdf.
       

112
photophotophotophotophoto
Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Solving the Tree Containment Problem for Genetically Stable Networks in Quadratic Time. In IWOCA15, Vol. 9538:197-208 of LNCS, springer, 2016.
Keywords: explicit network, from network, from rooted trees, genetically stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01226035 .
       

113
photophoto
Magnus Bordewich and Charles Semple. Reticulation-visible networks. In Advances in Applied Mathematics, Vol. 78:114-141, 2016.
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, tree containment.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS16.pdf.
       

114
photo
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.
       

115
photophotophotophoto
Vincent Ranwez, Celine Scornavacca, Jean-Philippe Doyon and Vincent Berry. Inferring gene duplications, transfers and losses can be done in a discrete framework. In JOMB, Vol. 72(7):1811-1844, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
       

116
photophoto
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.
       

117
photophotophotophotophoto
François Chevenet, Jean-Philippe Doyon, Celine Scornavacca, Edwin Jacox, Emmanuelle Jousselin and Vincent Berry. SylvX: a viewer for phylogenetic tree reconciliations. In BIO, Vol. 32(4):608-610, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program SylvX, software, visualization.
Note: https://www.researchgate.net/profile/Emmanuelle_Jousselin/publication/283446016_SylvX_a_viewer_for_phylogenetic_tree_reconciliations/links/5642146108aec448fa621efa.pdf.
       

118
photophoto
Rinku Mathur and Neeru Adlakha. A graph theoretic model for prediction of reticulation events and phylogenetic networks for DNA sequences. In Egyptian Journal of Basic and Applied Sciences, Vol. 3(3):263-271, 2016.
Keywords: from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1016/j.ejbas.2016.07.004.
       

119
photophotophoto
Andreas Gunawan, Bingxin Lu and Louxin Zhang. A program for verification of phylogenetic network models. In ECCB16, Vol. 32(17):i503-i510 of BIO, 2016.
Keywords: exponential algorithm, from network, from rooted trees, phylogenetic network, phylogeny, software, tree containment.
Note: http://dx.doi.org/10.1093/bioinformatics/btw467.
       

120
photophoto
Hussein A. Hejase and Kevin J. Liu. A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation. Vol. 17(422):1-12, 2016.
Keywords: abstract network, evaluation, from sequences, phylogenetic network, phylogeny, Program PhyloNet, Program PhyloNetworks SNaQ, reconstruction, simulation, unicyclic network.
Note: http://dx.doi.org/10.1186/s12859-016-1277-1.
       

121
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.
       

122
photo
Benjamin Albrecht. Computing Hybridization Networks Using Agreement Forests. PhD thesis, Ludwig-Maximilians-Universität München, 2016.
Note: https://edoc.ub.uni-muenchen.de/19444/.
       

123
photophotophotophotophoto
Philippe Gambette, Leo van Iersel, Steven Kelk, Fabio Pardi and Celine Scornavacca. Do branch lengths help to locate a tree in a phylogenetic network? In BMB, Vol. 78(9):1773-1795, 2016.
Keywords: branch length, explicit network, FPT, from network, from rooted trees, NP complete, phylogenetic network, phylogeny, pseudo-polynomial, time consistent network, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1607.06285.
       

124
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.
       

125
photo
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.
       

126
photo
Maria Anaya, Olga Anipchenko-Ulaj, Aisha Ashfaq, Joyce Chiu, Mahedi Kaiser, Max Shoji Ohsawa, Megan Owen, Ella Pavlechko, Katherine St. John, Shivam Suleria, Keith Thompson and Corrine Yap. On Determining if Tree-based Networks Contain Fixed Trees. In BMB, Vol. 78(5):961-969, 2016.
Keywords: explicit network, FPT, NP complete, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1602.02739.
       

127
photo
Momoko Hayamizu. On the existence of infinitely many universal tree-based networks. In JTB, Vol. 396:204-206, 2016.
Keywords: explicit network, phylogenetic network, phylogeny, tree-based network.
Note: http://arxiv.org/abs/1512.02402.
       

128
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.
       

129
photophotophoto
Dingqiao Wen, Yun Yu and Luay Nakhleh. Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent. In PLoS Genetics, Vol. 12(5):e1006006, 2016.
Keywords: bayesian, coalescent, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
       

130
photophoto
Jiafan Zhu, Yun Yu and Luay Nakhleh. In the Light of Deep Coalescence: Revisiting Trees Within Networks. In RECOMB-CG16, Vol. 17(suppl. 14):415.271-282 of BMCB, 2016.
Keywords: branch length, evaluation, explicit network, incomplete lineage sorting, phylogenetic network, phylogeny, statistical model, tree-based network, weakly displaying.
Note: http://arxiv.org/abs/1606.07350.
       

131
photophoto
Magnus Bordewich and Nihan Tokac. An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances. In DAM, Vol. 213:47-59, 2016.
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://dx.doi.org/10.1016/j.dam.2016.05.011.
       

132
photo
Mike Steel. Introduction to phylogenetic networks. In Phylogeny: Discrete and Random Processes in Evolution, Vol. 89 of CBMS-NSF Regional Conference Series in Applied Mathematics, Chapter 10, SIAM, 2016.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey.
Note: http://bookstore.siam.org/cb89/.
       

133
photo
Juan Wang. A Survey of Methods for Constructing Rooted Phylogenetic Networks. In PLoS ONE, Vol. 11(11):e0165834, 2016.
Keywords: evaluation, explicit network, from clusters, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, Program LNetwork, reconstruction, survey.
Note: http://dx.doi.org/10.1371/journal.pone.0165834.
       

134
photo
Nihan Tokac. Efficiency of Algorithms in Phylogenetics. PhD thesis, Durham University, U.K., 2016.
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://etheses.dur.ac.uk/11768/.
       

135
photophotophoto
Leo van Iersel, Steven Kelk and Celine Scornavacca. Kernelizations for the hybridization number problem on multiple nonbinary trees. In JCSS, Vol. 82(6):1075-1089, 2016.
Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction.
Note: https://arxiv.org/abs/1311.4045v3.
       

136
photo
Kristina Wicke. Extending the concept of phylogenetic diversity and its measures from trees to networks. Master's thesis, Ernst-Moritz-Arndt-Universität Greifswald, 2016.
Keywords: diversity, explicit network, from network, normal network, phylogenetic network, phylogeny.
Note: https://math-inf.uni-greifswald.de/fileadmin/uni-greifswald/fakultaet/mnf/mathinf/wicke/MasterThesis_KristinaWicke.pdf.
       

137
photophotophoto
Edwin Jacox, Cédric Chauve, Gergely J. Szöllösi, Yann Ponty and Celine Scornavacca. EcceTERA: comprehensive gene tree-species tree reconciliation using parsimony. In BIO, Vol. 32(13):2056-2058, 2016.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, parsimony, phylogenetic network, phylogeny, polynomial, Program ecceTERA.
Note: https://doi.org/10.1093/bioinformatics/btw105.
       

138
photo
Pei Wu. Quartet weights in phylogenetic network reconstruction. PhD thesis, University of Chinese Academy of Sciences, 2016.
Keywords: abstract network, from distances, from quartets, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: https://www.researchgate.net/publication/324475948_Quartet_weights_in_phylogenetic_network_reconstruction.
       

139
photo
Monika Balvociute. Flat Embeddings of Genetic and Distance Data. PhD thesis, University of Otago, 2016.
Keywords: abstract network, flat, phylogenetic network, phylogeny, planar, Program FlatNJ, Program SplitsTree, split, split network.
Note: http://hdl.handle.net/10523/6286.
       

140
photo
Dingqiao Wen. Bayesian Inference of Phylogenetic Networks. Master's thesis, Rice University, Texas, 2016.
Keywords: bayesian, explicit network, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
Note: https://scholarship.rice.edu/bitstream/handle/1911/96515/WEN-DOCUMENT-2016.pdf?sequence=1&isAllowed=y.
       

141
photophotophotophoto
Mareike Fischer, Leo van Iersel, Steven Kelk and Celine Scornavacca. On Computing The Maximum Parsimony Score Of A Phylogenetic Network. In SIDMA, Vol. 29(1):559-585, 2015.
Keywords: APX hard, cluster containment, explicit network, FPT, from network, from sequences, integer linear programming, level k phylogenetic network, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, Program MPNet, reconstruction, software.
Note: http://arxiv.org/abs/1302.2430.
       

142
photophotophoto
Colin McDiarmid, Charles Semple and Dominic Welsh. Counting phylogenetic networks. In Annals of Combinatorics, Vol. 19(1):205-224, 2015.
Keywords: counting, explicit network, normal network, phylogenetic network, phylogeny, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/MSW13.pdf.
       

143
photophoto
Andrew R. Francis and Mike Steel. Tree-like Reticulation Networks - When Do Tree-like Distances Also Support Reticulate Evolution? In MBIO, Vol. 259:12-19, 2015.
Keywords: from distances, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1405.2965.
       

144
photophotophotophoto
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.
       

145
photophoto
Andrew R. Francis and Mike Steel. Which phylogenetic networks are merely trees with additional arcs? In Systematic Biology, Vol. 64(5):768-777, 2015.
Keywords: explicit network, phylogenetic network, phylogeny, polynomial, tree-based network.
Note: http://arxiv.org/abs/1502.07045.
       

146
photophoto
Fabio Pardi and Celine Scornavacca. Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable. In PLoS Computational Biology, Vol. 11(4):e1007137.1-23, 2015.
Keywords: branch length, explicit network, from rooted trees, identifiability, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1371/journal.pcbi.1004135.
       

147
photophotophotophotophoto
Philippe Gambette, Andreas Gunawan, Anthony Labarre, Stéphane Vialette and Louxin Zhang. Locating a Tree in A Phylogenetic Network in Quadratic Time. In RECOMB15, Vol. 9029:96-107 of LNCS, Springer, 2015.
Keywords: evaluation, explicit network, from network, from rooted trees, genetically stable network, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
Note: https://hal.archives-ouvertes.fr/hal-01116231/en.
       

148
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.
       

149
photophoto
Quan Nguyen and Teemu Roos. Likelihood-based inference of phylogenetic networks from sequence data by PhyloDAG. In AlCoB15, Vol. 9199:126-140 of LNCS, springer, 2015.
Keywords: BIC, explicit network, from sequences, likelihood, phylogenetic network, phylogeny, Program PhyloDAG, reconstruction, software.
Note: http://www.cs.helsinki.fi/u/ttonteri/pub/alcob2015.pdf.
       

150
photo
Vladimir Ulyantsev and Mikhail Melnik. Constructing Parsimonious Hybridization Networks from Multiple Phylogenetic Trees Using a SAT-solver. In AlCoB15, Vol. 9199:141-153 of LNCS, springer, 2015.
Keywords: explicit network, from rooted trees, from trees, phylogenetic network, phylogeny, Program PIRN, reconstruction.
Note: https://www.researchgate.net/profile/Vladimir_Ulyantsev/publication/282816862_Constructing_Parsimonious_Hybridization_Networks_from_Multiple_Phylogenetic_Trees_Using_a_SAT-Solver/links/561d372c08aecade1acb3699/Constructing-Parsimonious-Hybridization-Networks-from-Multiple-Phylogenetic-Trees-Using-a-SAT-Solver.pdf.
       

151
photophotophoto
Jittat Fakcharoenphol, Tanee Kumpijit and Attakorn Putwattana. A Faster Algorithm for the Tree Containment Problem for Binary Nearly Stable Phylogenetic Networks. In Proceedings of the The 12th International Joint Conference on Computer Science and Software Engineering (JCSSE'15), Pages 337-342, IEEE, 2015.
Keywords: dynamic programming, explicit network, from network, from rooted trees, nearly-stable network, phylogenetic network, phylogeny, polynomial, tree containment.
       

152
photophoto
Misagh Kordi and Mukul S. Bansal. On the Complexity of Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees. In ISBRA15, Vol. 9096:187-198 of LNCS, springer, 2015.
Keywords: duplication, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://compbio.engr.uconn.edu/papers/Kordi_ISBRA2015.pdf.
       

153
photophoto
Yun Yu and Luay Nakhleh. A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. In ISBRA15, Vol. 9096:378-389 of LNCS, springer, 2015.
Keywords: bootstrap, explicit network, from distances, heuristic, incomplete lineage sorting, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/YuNakhleh-ISBRA15.pdf.
       

154
photo
Benjamin Albrecht. Computing all hybridization networks for multiple binary phylogenetic input trees. In BMCB, Vol. 16(236):1-15, 2015.
Keywords: agreement forest, explicit network, exponential algorithm, FPT, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, Program PIRN, reconstruction.
Note: http://dx.doi.org/10.1186/s12859-015-0660-7.
       

155
photophoto
Johannes Fischer and Daniel Peters. A Practical Succinct Data Structure for Tree-Like Graphs. In WALCOM15, Vol. 8973:65-76 of LNCS, springer, 2015.
Keywords: compression, from network, phylogenetic network, phylogeny.
       

156
photo
Ward C Wheeler. Phylogenetic network analysis as a parsimony optimization problem. In BMCB, Vol. 16(296):1-9, 2015.
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1186/s12859-015-0675-0.
       

157
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.
       

158
photophoto
Yun Yu and Luay Nakhleh. A maximum pseudo-likelihood approach for phylogenetic networks. In RECOMB-CG15, Vol. 16(Suppl 10)(S10):1-10 of BMC Genomics, BioMed Central, 2015.
Keywords: explicit network, from rooted trees, hybridization, incomplete lineage sorting, likelihood, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, tripartition distance.
Note: http://dx.doi.org/10.1186/1471-2164-16-S10-S10.
       

159
photophotophoto
Sha Zhu, James H. Degnan, Sharyn J. Goldstein and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. In BMCB, Vol. 16(292):1-7, 2015.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://dx.doi.org/10.1186/s12859-015-0721-y.
       

160
photophotophotophotophoto
Gergely J. Szöllösi, Adrián Arellano Davín, Eric Tannier, Vincent Daubin and Bastien Boussau. Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. In Philosophical Transactions of the Royal Society of London B: Biological Sciences, Vol. 370(1678):1-11, 2015.
Keywords: duplication, from sequences, lateral gene transfer, loss, phylogenetic network, phylogeny, Program ALE, reconstruction.
Note: http://dx.doi.org/10.1098/rstb.2014.0335.
       

161
photophoto
Thu-Hien To and Celine Scornavacca. Efficient algorithms for reconciling gene trees and species networks via duplication and loss events. In RECOMB-CG15, Vol. 16(Suppl 10)(S6):1-14 of BMC Genomics, BioMed Central, 2015.
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2164-16-S10-S6.
       

162
photophoto
Dwueng-Chwuan Jhwueng and Brian O'Meara. Trait Evolution on Phylogenetic Networks. 2015.
Keywords: explicit network, from network, hybridization, phylogenetic network, phylogeny, Program BMhyd, statistical model.
Note: http://dx.doi.org/10.1101/023986.
       

163
photophoto
Andreas Gunawan and Louxin Zhang. Bounding the Size of a Network Defined By Visibility Property. 2015.
Keywords: bound, explicit network, galled network, nearly-stable network, phylogenetic network, phylogeny, reticulation-visible network, stable-child network.
Note: http://arxiv.org/abs/1510.00115.
       

164
photophoto
Marc Thuillard and Didier Fraix-Burnet. Phylogenetic Trees and Networks Reduce to Phylogenies on Binary States: Does It Furnish an Explanation to the Robustness of Phylogenetic Trees against Lateral Transfers? In Evolutionary Bioinformatics, Vol. 11:213-221, 2015. [Abstract]
Keywords: circular split system, explicit network, from multistate characters, outerplanar, perfect, phylogenetic network, phylogeny, planar, polynomial, reconstruction, split.
Note: http://dx.doi.org/10.4137%2FEBO.S28158.
       

165
photo
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.
       

166
photo
Benjamin Albrecht. Computing a Relevant Set of Nonbinary Maximum Acyclic Agreement Forests. 2015.
Keywords: agreement forest, explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software.
Note: http://arxiv.org/abs/1512.05703.
       

167
photo
Benjamin Albrecht. Fast computation of all maximum acyclic agreement forests for two rooted binary phylogenetic trees. 2015.
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program Hybroscale, reconstruction, software.
Note: http://arxiv.org/abs/1512.05656.
       

168
photo
Nela Lekic. Trees, agreement forests and treewidth: combinatorial algorithms for constructing phylogenetic networks. PhD thesis, Maastricht University, The Netherlands, 2015.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.
       

169
photophoto
Jessica W. Leigh and David Bryant. PopART: full-feature software for haplotype network construction. In Methods in Ecology and Evolution, Vol. 6(9):1110-1116, 2015.
Keywords: abstract network, from sequences, haplotype network, MedianJoining, phylogenetic network, phylogeny, population genetics, Program PopART, Program TCS, software.
Note: http://dx.doi.org/10.1111/2041-210X.12410.
       

170
photophotophoto
Gabriel Cardona, Joan Carles Pons and Francesc Rosselló. A reconstruction problem for a class of phylogenetic networks with lateral gene transfers. In ALMOB, Vol. 10(28):1-15, 2015.
Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LGTnetwork, reconstruction, software, tree-based network.
Note: http://dx.doi.org/10.1186/s13015-015-0059-z.
       

171
photo
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.
       

172
photophotophotophoto
Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. The comparison of tree-sibling time consistent phylogenetic networks is graph-isomorphism complete. In The Scientific World Journal, Vol. 2014(254279):1-6, 2014.
Keywords: abstract network, distance between networks, from network, isomorphism, phylogenetic network, tree sibling network.
Note: http://arxiv.org/abs/0902.4640.
       
Toggle abstract
173
photophoto
Steven Kelk and Celine Scornavacca. Constructing minimal phylogenetic networks from softwired clusters is fixed parameter tractable. In ALG, Vol. 68(4):886-915, 2014.
Keywords: explicit network, FPT, from clusters, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1108.3653.
       
Toggle abstract
174
photophotophoto
Hadi Poormohammadi, Changiz Eslahchi and Ruzbeh Tusserkani. TripNet: A Method for Constructing Rooted Phylogenetic Networks from Rooted Triplets. In PLoS ONE, Vol. 9(9):e106531, 2014.
Keywords: explicit network, from triplets, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software.
Note: http://arxiv.org/abs/1201.3722.
       
Toggle abstract
175
photophoto
Sven Herrmann and Vincent Moulton. Computing the blocks of a quasi-median graph. In DAM, Vol. 179:129-138, 2014.
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, polynomial, Program QuasiDec, quasi-median network, reconstruction.
Note: http://arxiv.org/abs/1206.6135.
       

176
photophoto
Leo van Iersel and Vincent Moulton. Trinets encode tree-child and level-2 phylogenetic networks. In JOMB, Vol. 68(7):1707-1729, 2014.
Keywords: explicit network, from subnetworks, from trinets, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.0362.
       
Toggle abstract
177
photophoto
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.
       
Toggle abstract
178
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.
       

179
photophoto
Leo van Iersel and Steven Kelk. Kernelizations for the hybridization number problem on multiple nonbinary trees. In WG14, Vol. 8747:299-311 of LNCS, springer, 2014.
Keywords: explicit network, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Treeduce, reconstruction.
Note: http://arxiv.org/abs/1311.4045.
       

180
photophoto
Jesper Jansson and Andrzej Lingas. Computing the rooted triplet distance between galled trees by counting triangles. In Journal of Discrete Algorithms, Vol. 25:66-78, 2014.
Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny, polynomial, triplet distance.
       
Toggle abstract
181
photo
Ward C Wheeler. Phyletic groups on networks. In Cladistics, Vol. 30(4):447-451, 2014.
Keywords: explicit network, from network, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1111/cla.12062.
       
Toggle abstract
182
photophoto
Lavanya Kannan and Ward C Wheeler. Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming. In JCB, Vol. 21(4):303-319, 2014.
Keywords: explicit network, exponential algorithm, from network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
       
Toggle abstract
183
photophoto
Jialiang Yang, Stefan Grünewald, Yifei Xu and Xiu-Feng Wan. Quartet-based methods to reconstruct phylogenetic networks. In BMC Systems Biology, Vol. 80(21), 2014.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program QuartetMethods, Program QuartetNet, Program SplitsTree, reconstruction.
Note: http://dx.doi.org/10.1186/1752-0509-8-21 .
       
Toggle abstract
184
photophotophotophoto
Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S. Bansal and Manolis Kellis. Pareto-optimal phylogenetic tree reconciliation. In ISMB14, Vol. 30:i87-i95 of BIO, 2014.
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, polynomial, Program Xscape, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btu289.
       
Toggle abstract
185
photophotophotophotophoto
Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn and Luay Nakhleh. An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. In PLoS ONE, Vol. 10(6):e1003649, 2014.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program PhyloNet-HMM.
Note: http://arxiv.org/abs/1310.7989.
       
Toggle abstract
186
photo
David A. Morrison. Phylogenetic Networks: A Review of Methods to Display Evolutionary History. In Annual Research & Review in Biology, Vol. 4(10):1518-1543, 2014.
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction, survey.
       

187
photo
David A. Morrison. Rooted Phylogenetic Networks for Exploratory Data Analysis. In Advances in Research, Vol. 2(3):145-152, 2014.
Keywords: abstract network, explicit network, phylogenetic network, reconstruction.
       

188
photo
David A. Morrison. Next generation sequencing and phylogenetic networks. In EMBnet.journal, Vol. 20(e760):1-4, 2014.
Keywords: abstract network, from NGS data, phylogenetic network, phylogeny, Program SplitsTree, reconstruction.
       

189
photo
Dan Gusfield. ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. MIT Press, 2014.
Keywords: ARG, explicit network, phylogenetic network, phylogeny, survey.
Note: http://mitpress.mit.edu/books/recombinatorics.
       

190
photo
Josh Voorkamp né Collins. Untangling Evolution. PhD thesis, University of Otago, New Zealand, 2014.
Keywords: agreement forest, explicit network, from rooted trees, generation, phylogenetic network, phylogeny, reconstruction.
Note: http://otago.ourarchive.ac.nz/handle/10523/4802.
       

191
photophotophoto
Vladimir Makarenkov, Alix Boc and Pierre Legendre. A New Algorithm for Inferring Hybridization Events Based on the Detection of Horizontal Gene Transfers. In Fuad Aleskerov, Boris Goldengorin and Panos M. Pardalos editors, Clusters, Orders, and Trees: Methods and Applications, Vol. 92 of Springer Optimization and Its Applications, Springer, 2014.
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction.
       

192
photophotophotophoto
Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number for binary and nonbinary trees. In BMCB, Vol. 15(127):1-12, 2014.
Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, Program CycleKiller, Program TerminusEst, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2105-15-127.
       

193
photo
Yi-Chieh Wu. Computational evolutionary genomics : phylogenomic models spanning domains, genes, individuals, and species. PhD thesis, Massachusetts Institute of Technology, U.S.A., 2014.
Keywords: duplication, from sequences, from species tree, lateral gene transfer, loss, phylogeny, Program TreeFix-DTL, reconstruction.
Note: http://hdl.handle.net/1721.1/87937.
       

194
photophotophoto
Monika Balvociute, Andreas Spillner and Vincent Moulton. FlatNJ: A Novel Network-Based Approach to Visualize Evolutionary and Biogeographical Relationships. In Systematic Biology, Vol. 63(3):383-396, 2014.
Keywords: abstract network, flat, phylogenetic network, phylogeny, Program FlatNJ, Program SplitsTree, split network.
Note: http://dx.doi.org/10.1093/sysbio/syu001.
       
Toggle abstract
195
photophotophotophoto
Johann-Mattis List, Shijulal Nelson-Sathi, Hans Geisler and William Martin. Networks of lexical borrowing and lateral gene transfer in language and genome evolution. In BioEssays, Vol. 36(2):141-150, 2014.
Keywords: explicit network, minimal lateral network, phylogenetic network, Program lingpy.
Note: http://dx.doi.org/10.1002/bies.201300096.
       
Toggle abstract
196
photo
Benjamin Albrecht. Computing Hybridization Networks for Multiple Rooted Binary Phylogenetic Trees by Maximum Acyclic Agreement Forests. 2014.
Keywords: agreement forest, from rooted trees, minimum number, phylogenetic network, phylogeny, polynomial, Program Hybroscale, reconstruction.
Note: http://arxiv.org/abs/1408.3044.
       

197
photophoto
Puspal Bhabak and Asish Mukhopadhyay. A 3-factor approximation algorithm for a Minimum Acyclic Agreement Forest on k rooted, binary phylogenetic trees. 2014.
Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1407.7125.
       

198
photo
Zhijiang Li. Fixed-Parameter Algorithm for Hybridization Number of Two Multifurcating Trees. Master's thesis, Dalhousie University, Canada, 2014.
Keywords: agreement forest, explicit network, FPT, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://hdl.handle.net/10222/53976.
       

199
photo
Juan Wang. A new algorithm to construct phylogenetic networks from trees. In Genetics and Molecular Research, Vol. 13(1):1456-1464, 2014.
Keywords: explicit network, from clusters, heuristic, phylogenetic network, Program LNetwork, Program QuickCass, reconstruction.
Note: http://dx.doi.org/10.4238/2014.March.6.4.
       
Toggle abstract
200
photophotophoto
Matthieu Willems, Nadia Tahiri and Vladimir Makarenkov. A new efficient algorithm for inferring explicit hybridization networks following the Neighbor-Joining principle. In JBCB, Vol. 12(5), 2014.
Keywords: explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction.
       
Toggle abstract
201
photophotophoto
Paul Cordue, Simone Linz and Charles Semple. Phylogenetic Networks that Display a Tree Twice. In BMB, Vol. 76(10):2664-2679, 2014.
Keywords: from rooted trees, normal network, phylogenetic network, phylogeny, reconstruction, tree-child network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/CLS14.pdf.
       
Toggle abstract
202
photophoto
Riccardo Dondi and Yuri Pirola. Beyond Evolutionary Trees. In Ming-Yang Kao editor, Encyclopedia of Algorithms, Pages 1-7, Springer, 2014.
Keywords: explicit network, phylogenetic network, phylogeny, reconstruction, survey.
       

203
photo
Josh Voorkamp né Collins. Maximal Acyclic Agreement Forests. In JCB, Vol. 21(10):723-731, 2014.
Keywords: agreement forest, explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
       

204
photo
Yun Yu. Models and Methods for Evolutionary Histories Involving Hybridization and Incomplete Lineage Sorting. PhD thesis, Rice University, U.S.A., 2014.
Keywords: hybridization, incomplete lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
Note: http://hdl.handle.net/1911/77583.
       

205
photophotophoto
Yun Yu, Jianrong Dong, Kevin J. Liu and Luay Nakhleh. Maximum likelihood inference of reticulate evolutionary histories. In PNAS, Vol. 111(46):16448-16453, 2014.
Keywords: explicit network, likelihood, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1073/pnas.1407950111.
       

206
photo
Julia Matsieva. A Static Formulation of the History Bound Problem. Master's thesis, UC Davis, 2014.
Keywords: bound, dynamic programming, explicit network, from binary characters, from clusters, phylogenetic network, phylogeny, polynomial.
Note: https://escholarship.org/uc/item/3741t064.
       

207
photophotophotophotophotophoto
Joel Sjöstrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad and Jens Lagergren. A Bayesian Method for Analyzing Lateral Gene Transfer. In Systematic Biology, Vol. 63(3):409-420, 2014.
Keywords: bayesian, duplication, from rooted trees, from sequences, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program JPrIME-DLTRS, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syu007.
       

208
photophotophotophoto
Adrià Alcalà Mena, Mercè Llabrés, Francesc Rosselló and Pau Rullan. Tree-Child Cluster Networks. In Fundamenta Informaticae, Vol. 134(1-2):1-15, 2014.
Keywords: explicit network, from clusters, phylogenetic network, phylogeny, Program PhyloNetwork, reconstruction, tree-child network.
       

209
photo
David A. Morrison. Is the Tree of Life the Best Metaphor, Model, or Heuristic for Phylogenetics? In Systematic Biology, Vol. 63(4):628-638, 2014.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey.
       

210
photophotophoto
Leo van Iersel, Celine Scornavacca and Steven Kelk. Exact reconciliation of undated trees. 2014.
Keywords: duplication, explicit network, integer linear programming, loss, phylogenetic network, phylogeny, Program ILPEACE, reconstruction.
Note: https://arxiv.org/abs/1410.7004.
       

211
photophoto
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
212
photophoto
Leo van Iersel and Simone Linz. A quadratic kernel for computing the hybridization number of multiple trees. In IPL, Vol. 113:318-323, 2013.
Keywords: explicit network, FPT, from rooted trees, kernelization, minimum number, phylogenetic network, phylogeny, Program Clustistic, Program MaafB, Program PIRN, reconstruction.
Note: http://arxiv.org/abs/1203.4067, poster.
       
Toggle abstract
213
photophotophoto
Chris Whidden, Robert G. Beiko and Norbert Zeh. Fixed-Parameter Algorithms for Maximum Agreement Forests. In SICOMP, Vol. 42(4):1431-1466, 2013.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance.
Note: http://arxiv.org/abs/1108.2664, slides.
       
Toggle abstract
214
photophotophotophotophoto
Stefan Grünewald, Andreas Spillner, Sarah Bastkowski, Anja Bögershausen and Vincent Moulton. SuperQ: Computing Supernetworks from Quartets. In TCBB, Vol. 10(1):151-160, 2013.
Keywords: abstract network, circular split system, from quartets, heuristic, phylogenetic network, phylogeny, Program QNet, Program SplitsTree, Program SuperQ, software, split network.
       
Toggle abstract
215
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
216
photophotophoto
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
217
photo
Yufeng Wu. An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. In RECOMB13, Vol. 7821:291-303 of LNCS, springer, 2013.
Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program PIRN, reconstruction.
Note: http://www.engr.uconn.edu/~ywu/Papers/ExactNetRecomb2013.pdf.
       
Toggle abstract
218
photophotophoto
Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In RECOMB13, Vol. 7821:1-13 of LNCS, springer, 2013.
Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, polynomial, Program RANGER-DTL, reconstruction.
Note: http://people.csail.mit.edu/mukul/Bansal_RECOMB2013.pdf.
       
Toggle abstract
219
photo
Miguel Arenas. Computer programs and methodologies for the simulation of DNA sequence data with recombination. In Frontiers in Genetics, Vol. 4(9), 2013.
Keywords: explicit network, phylogenetic network, phylogeny, simulation.
Note: http://dx.doi.org/10.3389%2Ffgene.2013.00009.
       

220
photophotophoto
Sha Zhu, James H. Degnan and Bjarki Eldon. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees. 2013.
Keywords: explicit network, from network, phylogenetic network, phylogeny, Program Hybrid-Lambda, simulation, software.
Note: http://arxiv.org/abs/1303.0673.
       

221
photophoto
Jialiang Yang, Stefan Grünewald and Xiu-Feng Wan. Quartet-Net: A Quartet Based Method to Reconstruct Phylogenetic Networks. In MBE, Vol. 30(5):1206-1217, 2013.
Keywords: from quartets, phylogenetic network, phylogeny, Program QuartetNet, reconstruction.
       
Toggle abstract
222
photophotophotophotophoto
Thi-Hau Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Chifolleau Arigon, Jean-Philippe Doyon and Vincent Berry. Reconciliation and local gene tree rearrangement can be of mutual profit. In ALMOB, Vol. 8(12), 2013.
Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, Program Prunier, reconstruction, software.
       
Toggle abstract
223
photophotophotophotophoto
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.
       

224
photophotophoto
Simone Linz, Katherine St. John and Charles Semple. Counting trees in a phylogenetic network is #P-complete. In SICOMP, Vol. 42(4):1768-1776, 2013.
Keywords: counting, from network, phylogenetic network, phylogeny.
Note: http://ab.inf.uni-tuebingen.de/people/linz/publications/counting.pdf.
       

225
photophotophotophotophotophotophotophotophotophotophoto
Eric Bapteste, Leo van Iersel, Axel Janke, Scott Kelchner, Steven Kelk, James O. McInerney, David A. Morrison, Luay Nakhleh, Mike Steel, Leen Stougie and James B. Whitfield. Networks: expanding evolutionary thinking. In Trends in Genetics, Vol. 29(8):439-441, 2013.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction.
Note: http://bioinf.nuim.ie/wp-content/uploads/2013/06/Bapteste-TiG-2013.pdf.
       
Toggle abstract
226
photophotophoto
Yun Yu, R. Matthew Barnett and Luay Nakhleh. Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting. In Systematic Biology, Vol. 62(5):738-751, 2013.
Keywords: from network, from rooted trees, hybridization, lineage sorting, parsimony, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
       
Toggle abstract
227
photophotophotophotophoto
Juan Wang, Maozu Guo, Xiaoyan Liu, Yang Liu, Chunyu Wang, Linlin Xing and Kai Che. LNETWORK: An Efficient and Effective Method for Constructing Phylogenetic Networks. In BIO, Vol. 29(18):2269-2276, 2013.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, Program LNetwork, reconstruction, software.
       
Toggle abstract
228
photophotophotophoto
Juan Wang, Maozu Guo, Linlin Xing, Kai Che, Xiaoyan Liu and Chunyu Wang. BIMLR: A Method for Constructing Rooted Phylogenetic Networks from Rooted Phylogenetic Trees. In Gene, Vol. 527(1):344-351, 2013.
Keywords: explicit network, from clusters, from rooted trees, phylogenetic network, phylogeny, Program BIMLR, Program Dendroscope, reconstruction, software.
       
Toggle abstract
229
photophoto
Zhi-Zhong Chen and Lusheng Wang. An Ultrafast Tool for Minimum Reticulate Networks. In JCB, Vol. 20(1):38-41, 2013.
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program ultra-Net, reconstruction.
Note: http://www.cs.cityu.edu.hk/~lwang/research/jcb2013.pdf.
       
Toggle abstract
230
photo
Simone Linz. Reticulation. In Brenner's Encyclopedia of Genetics (Second Edition), 2013.
Keywords: phylogenetic network, phylogeny, survey.
       

231
photophotophoto
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
232
photo
Willem Sonke. Reconstructing a level-1-network from quartets. 2013.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program Fylogenetica, reconstruction, software, visualization.
Note: http://alexandria.tue.nl/extra1/afstversl/wsk-i/sonke2013.pdf.
       

233
photophotophoto
Alexey A. Morozov, Yuri P. Galachyants and Yelena V. Likhoshway. Inferring Phylogenetic Networks from Gene Order Data. In BMRI, Vol. 2013(503193):1-7, 2013.
Keywords: abstract network, from distances, from gene order, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split decomposition, split network.
       
Toggle abstract
234
photophotophoto
Celine Scornavacca, Paprotny Wojciech, Vincent Berry and Vincent Ranwez. Representing a set of reconciliations in a compact way. In JBCB, Vol. 11(2):1250025, 2013.
Keywords: duplication, explicit network, from network, from rooted trees, from species tree, phylogeny, Program GraphDTL, Program TERA, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00818801.
       
Toggle abstract
235
photo
Thi-Hau Nguyen. Réconciliations: corriger des arbres de gènes et inférer la fiabilité des événements évolutifs. PhD thesis, Université Montpellier 2, France, 2013.
Keywords: duplication, explicit network, from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program Mowgli, Program MowgliNNI, reconstruction.
Note: http://www.biu-montpellier.fr/florabium/servlet/DocumentFileManager?source=ged&document=ged:IDOCS:247665&resolution=&recordId=theses%3ABIU_THESE%3A1789&file=.
       

236
photo
Luay Nakhleh. Computational approaches to species phylogeny inference and gene tree reconciliation. In Trends in Ecology and Evolution, Vol. 28(12):719-728, 2013.
Keywords: from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction, survey.
Note: http://bioinfo.cs.rice.edu/sites/bioinfo.cs.rice.edu/files/TREE-Nakhleh13.pdf.
       
Toggle abstract
237
photophotophoto
Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss. In JCB, Vol. 20(10):738-754, 2013.
Keywords: duplication, from rooted trees, from species tree, loss, phylogenetic network, phylogeny, Program RANGER-DTL, reconstruction.
Note: http://www.engr.uconn.edu/~mukul/Bansal_JCB2013.pdf.
       
Toggle abstract
238
photo
David A. Morrison. Phylogenetic networks are fundamentally different from other kinds of biological networks. In WenJun Zhang editor, Network Biology: Theories, Methods and Applications, Chapter 2, Nova Publishers, 2013.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny.
       

239
photophotophoto
Steven Kelk, Simone Linz and David A. Morrison. Fighting network space: it is time for an SQL-type language to filter phylogenetic networks. 2013.
Keywords: database, explicit network, from network, phylogenetic network, phylogeny.
Note: http://arxiv.org/abs/1310.6844.
       

240
photophotophotophoto
Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie. A short note on exponential-time algorithms for hybridization number. 2013.
Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1312.1255.
       

241
photophotophoto
Yun Yu, Nikola Ristic and Luay Nakhleh. Fast algorithms and heuristics for phylogenomics under ILS and hybridization. In RECOMB-CG'13, Vol. 14(Suppl 15):S6 of BMCB, 2013.
Keywords: from network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program PhyloNet, reconstruction.
       

242
photophotophotophoto
Alberto Apostolico, Matteo Comin, Andreas W. M. Dress and Laxmi Parida. Ultrametric networks: a new tool for phylogenetic analysis. In Algorithms for Molecular Biology, Vol. 8(7):1-10, 2013.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program Ultranet.
Note: http://dx.doi.org/10.1186/1748-7188-8-7.
       
Toggle abstract
243
photophotophoto
Mehdi Layeghifard, Pedro R. Peres-Neto and Vladimir Makarenkov. Inferring explicit weighted consensus networks to represent alternative evolutionary histories. In BMCEB, Vol. 13(274):1-25, 2013.
Keywords: explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, Program ConsensusNetwork, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-13-274.
       
Toggle abstract
244
photophotophotophoto
Gergely J. Szöllösi, Eric Tannier, Nicolas Lartillot and Vincent Daubin. Lateral Gene Transfer from the Dead. In Systematic Biology, Vol. 62(3):386-397, 2013.
Keywords: duplication, lateral gene transfer, likelihood, loss, phylogeny, Program TERA, reconstruction.
Note: http://dx.doi.org/10.1093/sysbio/syt003.
       
Toggle abstract
245
photophotophotophotophoto
Gergely J. Szöllösi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier and Vincent Daubin. Efficient Exploration of the Space of Reconciled Gene Trees. In Systematic Biology, Vol. 62(6):901-912, 2013.
Keywords: duplication, explicit network, lateral gene transfer, likelihood, loss, phylogeny, Program ALE, reconstruction.
Note: http://arxiv.org/abs/1306.2167.
       
Toggle abstract
246
photo
Chris Whidden. Efficient Computation and Application of Maximum Agreement Forests. PhD thesis, Dalhousie University, Canada, 2013.
Keywords: agreement forest, explicit network, FPT, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://hdl.handle.net/10222/35349.
       

247
photo
Yufeng Wu. An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees. In JCB, Vol. 20(10):792-804, 2013.
Keywords: explicit network, exponential algorithm, from rooted trees, phylogenetic network, phylogeny, Program PIRN, reconstruction.
       

248
photophotophoto
Yao-ban Chan, Vincent Ranwez and Celine Scornavacca. Reconciliation-based detection of co-evolving gene families. In BMC Bioinformatics, Vol. 14(332):1-9, 2013.
Keywords: cophylogeny, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2105-14-332.
       

249
photo
Sarah Bastkowski. From Trees to Networks and Back. PhD thesis, University of East Anglia, 2013.
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/_downloads/spectre_bastkowskis_thesis.pdf.
       

250
photophoto
Yun Yu and Luay Nakhleh. Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting. 2012.
Keywords: hybridization, lineage sorting, phylogenetic network, phylogeny, Program PhyloNet, reconstruction, software.
Note: http://arxiv.org/abs/1212.1909.
       

251
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
252
photo
Stephen J. Willson. CSD Homomorphisms Between Phylogenetic Networks. In TCBB, Vol. 9(4), 2012.
Keywords: explicit network, from network, from quartets, phylogenetic network.
Note: http://www.public.iastate.edu/~swillson/Relationships11IEEE.pdf, preliminary version entitled Relationships Among Phylogenetic Networks.
       
Toggle abstract
253
photophotophoto
Steven Kelk, Celine Scornavacca and Leo van Iersel. On the elusiveness of clusters. In TCBB, Vol. 9(2):517-534, 2012.
Keywords: explicit network, from clusters, from rooted trees, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, Program Clustistic, reconstruction, software.
Note: http://arxiv.org/abs/1103.1834.
       

254
photophoto
Hadi Poormohammadi and Changiz Eslahchi. Constructing Rooted Phylogenetic Networks from Triplets based on Height Function. In International Journal of Emerging Technology and Advanced Engineering, Vol. 2(7):389-393, 2012.
Keywords: from triplets, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.ijetae.com/files/Volume2Issue7/IJETAE_0712_67.pdf.
       

255
photophotophoto
Jeremy G. Sumner, Barbara R. Holland and Peter D. Jarvis. The algebra of the general Markov model on phylogenetic trees and networks. In BMB, Vol. 74(4):858-880, 2012.
Keywords: abstract network, phylogenetic network, phylogeny, split, split network, statistical model.
Note: http://arxiv.org/abs/1012.5165.
       
Toggle abstract
256
photophotophoto
Andreas Spillner, Binh T. Nguyen and Vincent Moulton. Constructing and Drawing Regular Planar Split Networks. In TCBB, Vol. 9(2):395-407, 2012.
Keywords: abstract network, from splits, phylogenetic network, phylogeny, reconstruction, visualization.
Note: slides and presentation available at http://www.newton.ac.uk/programmes/PLG/seminars/062111501.html.
       
Toggle abstract
257
photophoto
Paul Phipps and Sergey Bereg. Optimizing Phylogenetic Networks for Circular Split Systems. In TCBB, Vol. 9(2):535-547, 2012.
Keywords: abstract network, from distances, from splits, phylogenetic network, phylogeny, Program PhippsNetwork, reconstruction, software.
       
Toggle abstract
258
photophoto
Andreas Spillner and Vincent Moulton. Optimal algorithms for computing edge weights in planar split-networks. In Journal of Applied Mathematics and Computing, Vol. 39(1-2):1-13, 2012.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: http://dx.doi.org/10.1007/s12190-011-0506-z.
       
Toggle abstract
259
photophoto
Magnus Bordewich and Charles Semple. Budgeted Nature Reserve Selection with diversity feature loss and arbitrary split systems. In JOMB, Vol. 64(1):69-85, 2012.
Keywords: abstract network, approximation, diversity, phylogenetic network, polynomial, split network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS11.pdf.
       
Toggle abstract
260
photophotophoto
Celine Scornavacca, Simone Linz and Benjamin Albrecht. A fi rst step towards computing all hybridization networks for two rooted binary phylogenetic trees. In JCB, Vol. 19:1227-1242, 2012.
Keywords: agreement forest, explicit network, FPT, from rooted trees, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction.
Note: http://arxiv.org/abs/1109.3268.
       
Toggle abstract
261
photophoto
Zhi-Zhong Chen and Lusheng Wang. Algorithms for Reticulate Networks of Multiple Phylogenetic Trees. In TCBB, Vol. 9(2):372-384, 2012.
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CMPT, Program MaafB, reconstruction, software.
Note: http://rnc.r.dendai.ac.jp/~chen/papers/rMaaf.pdf.
       
Toggle abstract
262
photophotophotophotophoto
Changiz Eslahchi, Reza Hassanzadeh, Ehsan Mottaghi, Mahnaz Habibi, Hamid Pezeshk and Mehdi Sadeghi. Constructing circular phylogenetic networks from weighted quartets using simulated annealing. In MBIO, Vol. 235(2):123-127, 2012.
Keywords: abstract network, from quartets, heuristic, phylogenetic network, phylogeny, Program SAQ-Net, Program SplitsTree, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.mbs.2011.11.003.
       
Toggle abstract
263
photophotophotophoto
Benjamin Albrecht, Celine Scornavacca, Alberto Cenci and Daniel H. Huson. Fast computation of minimum hybridization networks. In BIO, Vol. 28(2):191-197, 2012.
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program Dendroscope, Program Hybroscale, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btr618.
       
Toggle abstract
264
photophotophotophotophotophoto
Steven Kelk, Leo van Iersel, Nela Lekic, Simone Linz, Celine Scornavacca and Leen Stougie. Cycle killer... qu'est-ce que c'est? On the comparative approximability of hybridization number and directed feedback vertex set. In SIDMA, Vol. 26(4):1635-1656, 2012.
Keywords: agreement forest, approximation, explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, Program CycleKiller, reconstruction.
Note: http://arxiv.org/abs/1112.5359, about the title.
       
Toggle abstract
265
photophotophoto
Philippe Gambette, Vincent Berry and Christophe Paul. Quartets and Unrooted Phylogenetic Networks. In JBCB, Vol. 10(4):1250004, 2012.
Keywords: abstract network, circular split system, explicit network, from quartets, level k phylogenetic network, orientation, phylogenetic network, phylogeny, polynomial, reconstruction, split, split network.
Note: http://hal.archives-ouvertes.fr/hal-00678046/en/.
       
Toggle abstract
266
photophotophoto
Yun Yu, James H. Degnan and Luay Nakhleh. The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection. In PLoS Genetics, Vol. 8(4):e1002660, 2012.
Keywords: AIC, BIC, explicit network, hybridization, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1371/journal.pgen.1002660.
       
Toggle abstract
267
photophoto
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.
       
Toggle abstract
268
photophoto
Pawel Górecki and Jerzy Tiuryn. Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model. In Logic and Program Semantics, Vol. 7230:83-105 of LNCS, springer, 2012.
Keywords: duplication, explicit network, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-642-29485-3_7.
       
Toggle abstract
269
photophotophotophotophoto
Bonnie Kirkpatrick, Yakir Reshef, Hilary Finucane, Haitao Jiang, Binhai Zhu and Richard M. Karp. Comparing Pedigree Graphs. In JCB, Vol. 19(9):998-1014, 2012.
Keywords: distance between networks, from network, pedigree.
Note: http://arxiv.org/abs/1009.0909, preliminary version as poster at WABI 2010.
       
Toggle abstract
270
photophotophoto
Mukul S. Bansal, Eric J. Alm and Manolis Kellis. Efficient Algorithms for the Reconciliation Problem with Gene Duplication, Horizontal Transfer, and Loss. In ISMB12, Vol. 28(12):i283-i291 of BIO, 2012.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Angst, Program Mowgli, Program RANGER-DTL, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/bts225.
       
Toggle abstract
271
photophotophotophotophoto
An-Chiang Chu, Jesper Jansson, Richard Lemence, Alban Mancheron and Kun-Mao Chao. Asymptotic Limits of a New Type of Maximization Recurrence with an Application to Bioinformatics. In TAMC12, Vol. 7287:177-188 of LNCS, springer, 2012.
Keywords: from triplets, galled network, level k phylogenetic network, phylogenetic network.
Note: preliminary version.
       
Toggle abstract
272
photophotophoto
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.
       
Toggle abstract
273
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
274
photophotophotophotophoto
Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster computation of the Robinson–Foulds distance between phylogenetic networks. In Information Sciences, Vol. 197:77-90, 2012.
Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.
       
Toggle abstract
275
photophotophotophoto
Leo van Iersel, Steven Kelk, Nela Lekic and Celine Scornavacca. A practical approximation algorithm for solving massive instances of hybridization number. In WABI12, Vol. 7534(430-440) of LNCS, springer, 2012.
Keywords: agreement forest, approximation, explicit network, from rooted trees, hybridization, phylogenetic network, phylogeny, Program CycleKiller, Program Dendroscope, Program HybridNET, reconstruction, software.
Note: http://arxiv.org/abs/1205.3417.
       
Toggle abstract
276
photophoto
Lavanya Kannan and Ward C Wheeler. Maximum Parsimony on Phylogenetic Networks. In ALMOB, Vol. 7:9, 2012.
Keywords: dynamic programming, explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1186/1748-7188-7-9.
       
Toggle abstract
277
photophotophoto
Alix Boc, Alpha B. Diallo and Vladimir Makarenkov. T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks. In NAR, Vol. 40(W1):W573-W579, 2012.
Keywords: from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software.
Note: http://dx.doi.org/10.1093/nar/gks485.
       
Toggle abstract
278
photophoto
Daniel H. Huson and Celine Scornavacca. Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks. In Systematic Biology, Vol. 61(6):1061-1067, 2012.
Keywords: from rooted trees, from triplets, phylogenetic network, phylogeny, Program Dendroscope, reconstruction, software, visualization.
       
Toggle abstract
279
photophoto
Hyun Jung Park and Luay Nakhleh. Inference of reticulate evolutionary histories by maximum likelihood: The performance of information criteria. In RECOMB-CG'12, Vol. 13(suppl 19):S12 of BMCB, 2012.
Keywords: AIC, BIC, explicit network, heuristic, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://www.biomedcentral.com/1471-2105/13/S19/S12.
       

280
photophoto
Zhi-Zhong Chen, Lusheng Wang and Satoshi Yamanaka. A fast tool for minimum hybridization networks. In BMCB, Vol. 13:155, 2012.
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, Program FastHN, reconstruction, software.
Note: http://dx.doi.org/10.1186/1471-2105-13-155.
       
Toggle abstract
281
photophoto
Michel Habib and Thu-Hien To. Constructing a Minimum Phylogenetic Network from a Dense Triplet Set. In JBCB, Vol. 10(5):1250013, 2012.
Keywords: explicit network, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1103.2266.
       
Toggle abstract
282
photophoto
Ruogu Sheng and Sergey Bereg. Approximating Metrics with Planar Boundary-Labeled Phylogenetic Networks. In JBCB, Vol. 10(6):1250017, 2012.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction.
       
Toggle abstract
283
photophotophotophotophoto
Maureen Stolzer, Han Lai, Minli Xu, Deepa Sathaye, Benjamin Vernot and Dannie Durand. Inferring Duplications, Losses, Transfers, and Incomplete Lineage Sorting with Non-Binary Species Trees. In ECCB12, Vol. 28(18):i409-i415 of BIO, 2012.
Keywords: duplication, explicit network, from rooted trees, lateral gene transfer, loss, phylogenetic network, phylogeny, Program Notung, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/bts386.
       
Toggle abstract
284
photo
Hyun Jung Park. Towards Accurate Reconstruction of Phylogenetic Networks. PhD thesis, Rice University, U.S.A., 2012.
Keywords: explicit network, likelihood, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://scholarship.rice.edu/handle/1911/64705.
       

285
photo
Devin Robert Bickner. On normal networks. PhD thesis, Iowa State University, U.S.A., 2012.
Keywords: distance between networks, explicit network, from network, from trees, normal network, phylogenetic network, phylogeny, polynomial, reconstruction, SPR distance.
Note: http://gradworks.umi.com/3511361.pdf.
       

286
photophoto
Adrià Alcalà Mena and Francesc Rosselló. Ternary graph isomorphism in polynomial time, after Luks. 2012.
Keywords: distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE.
Note: http://arxiv.org/abs/1209.0871.
       

287
photo
Adrià Alcalà Mena. Trivalent Graph isomorphism in polynomial time. Master's thesis, Universidad de Cantabria, Spain, 2012.
Keywords: distance between networks, explicit network, from network, isomorphism, phylogenetic network, phylogeny, polynomial, Program SAGE.
Note: http://arxiv.org/abs/1209.1040.
       

288
photophoto
Joseph K. Pickrell and Jonathan K. Pritchard. Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data. In PLoS Genetics, Vol. 8(11):e1002967, 2012.
Keywords: explicit network, heuristic, likelihood, phylogenetic network, phylogeny, population genetics, Program TreeMix.
Note: http://dx.doi.org/10.1371/journal.pgen.1002967.
       
Toggle abstract
289
photophotophotophoto
Nick J. Patterson, Priya Moorjani, Yontao Luo, Swapan Mallick, Nadin Rohland, Yiping Zhan, Teri Genschoreck, Teresa Webster and David Reich. Ancient Admixture in Human History. In Genetics, Vol. 192(3):1065-1093, 2012.
Keywords: explicit network, phylogenetic network, phylogeny, population genetics, Program AdmixTools.
Note: http://genetics.med.harvard.edu/reich/Reich_Lab/Welcome_files/2012_Patterson_AncientAdmixture_Genetics.pdf.
       
Toggle abstract
290
photophotophotophoto
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
291
photo
Cayla McBee. Generalizing Fourier Calculus on Evolutionary Trees to Splits Networks. In ISPAN'12, Pages 149-155, 2012.
Keywords: abstract network, from sequences, phylogenetic network, phylogeny, split network, statistical model.
       
Toggle abstract
292
photo
Alix Boc. Détection des transferts horizontaux de gènes : modèles et algorithmes appliqués à l'évolution des espèces et des langues. PhD thesis, Université du Québec à Montréal, Canada, 2012.
Keywords: explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, Program T REX, reconstruction.
Note: http://www.collectionscanada.gc.ca/obj/thesescanada/vol2/QMUQ/TC-QMUQ-4658.pdf.
       

293
photophotophoto
Fenglou Mao, David Williams, Olga Zhaxybayeva, Maria S. Poptsova, Pascal Lapierre, J. Peter Gogarten and Ying Xu. Quartet decomposition server: a platform for analyzing phylogenetic trees. In BMCB, Vol. 13:123, 2012.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, Program Quartet Decomposition, reconstruction, software, split network.
       
Toggle abstract
294
photophoto
Donovan H. Parks and Robert G. Beiko. Measuring Community Similarity with Phylogenetic Networks. In MBE, Vol. 29(12):3947-3958, 2012.
Keywords: abstract network, diversity, phylogenetic network, phylogeny, split network.
Note: poster available at http://dparks.wdfiles.com/local--files/publications/SMBE_BetaDiversity_2011.pdf.
       
Toggle abstract
295
photophotophoto
Zhi-Zhong Chen, Fei Deng and Lusheng Wang. Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers. In TCBB, Vol. 9(5):1515-1528, 2012.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.cityu.edu.hk/~lwang/research/tcbb2012c.pdf.
       
Toggle abstract
296
photo
Matthieu Willems. Un nouvel algorithme pour l'inférence de réseaux d'hybridation. Master's thesis, Université du Québec à Montréal, Canada, 2012.
Keywords: explicit network, from distances, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.archipel.uqam.ca/5015/.
       

297
photophoto
Daniel H. Huson and Celine Scornavacca. A survey of combinatorial methods for phylogenetic networks. In Genome Biology and Evolution, Vol. 3:23-35, 2011.
Keywords: phylogenetic network, survey.
Note: http://dx.doi.org/10.1093/gbe/evq077.
       
Toggle abstract
298
photophotophoto
Ali Tofigh, Mike Hallett and Jens Lagergren. Simultaneous Identification of Duplications and Lateral Gene Transfers. In TCBB, Vol. 8(2):517-535, 2011.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1109/TCBB.2010.14.
       
Toggle abstract
299
photophoto
Dan Levy and Lior Pachter. The Neighbor-Net Algorithm. In Advances in Applied Mathematics, Vol. 47(2):240-258, 2011.
Keywords: abstract network, circular split system, evaluation, from distances, NeighborNet, phylogenetic network, phylogeny, split network.
Note: http://arxiv.org/abs/math/0702515.
       
Toggle abstract
300
photophotophotophoto
Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Comparison of Galled Trees. In TCBB, Vol. 8(2):410-427, 2011.
Note: http://arxiv.org/abs/0906.1166.
       
Toggle abstract
301
photophotophoto
Daniel H. Huson, Regula Rupp and Celine Scornavacca. Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge University Press, 2011.
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.phylogenetic-networks.org/, buy at Amazon.com. Reviews here and there.
       

302
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
303
photophotophoto
Josh Voorkamp né Collins, Simone Linz and Charles Semple. Quantifying hybridization in realistic time. In JCB, Vol. 18(10):1305-1318, 2011.
Keywords: explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, software.
Note: http://wwwcsif.cs.ucdavis.edu/~linzs/CLS10_interleave.pdf, software available at http://www.math.canterbury.ac.nz/~c.semple/software.shtml.
       
Toggle abstract
304
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
305
photophotophotophotophoto
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/.
       
Toggle abstract
306
photophoto
Leo van Iersel and Steven Kelk. When two trees go to war. In JTB, Vol. 269(1):245-255, 2011.
Keywords: APX hard, explicit network, from clusters, from rooted trees, from sequences, from triplets, level k phylogenetic network, minimum number, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1004.5332.
       
Toggle abstract
307
photophotophoto
Mukul S. Bansal, J. Peter Gogarten and Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10), Vol. 6398:109-120 of LNCS, springer, 2011.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.cs.iastate.edu/~bansal/Highways_RCG10.pdf.
       
Toggle abstract
308
photophotophotophoto
Ruzbeh Tusserkani, Changiz Eslahchi, Hadi Poormohammadi and Azin Azadi. TripNet: A Method for Constructing Phylogenetic Networks from Triplets. 2011.
Keywords: explicit network, heuristic, level k phylogenetic network, phylogenetic network, phylogeny, Program TripNet, reconstruction, software.
Note: http://arxiv.org/abs/1104.4720.
       

309
photo
Klaus Schliep. Phangorn: Phylogenetic analysis in R. In Bioinformatics, Vol. 27(4):592-593, 2011.
Keywords: abstract network, from distances, phylogenetic network, Program Phangorn, software, split, split network.
Note: http://dx.doi.org/10.1093/bioinformatics/btq706.
       
Toggle abstract
310
photophotophotophoto
Yun Yu, Cuong Than, James H. Degnan and Luay Nakhleh. Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting. In Systematic Biology, Vol. 60(2):138-149, 2011.
Keywords: coalescent, hybridization, lineage sorting, reconstruction, statistical model.
Note: http://www.cs.rice.edu/~nakhleh/Papers/YuEtAl-SB11.pdf.
       
Toggle abstract
311
photophoto
Celine Scornavacca, Franziska Zickmann and Daniel H. Huson. Tanglegrams for Rooted Phylogenetic Trees and Networks. In ISMB11, Vol. 27(13):i248-i256 of BIO, 2011.
Keywords: from network, heuristic, integer linear programming, phylogenetic network, phylogeny, Program Dendroscope, tanglegram, visualization.
Note: http://dx.doi.org/10.1093/bioinformatics/btr210.
       
Toggle abstract
312
photophoto
Gergely J. Szöllösi and Vincent Daubin. Modeling Gene Family Evolution and Reconciling Phylogenetic Discord. In Evolutionary Genomics, Statistical and Computational Methods, Volume 2, Methods in Molecular Biology, Vol. 856:29-51, Chapter 2, springer, 2011.
Keywords: duplication, from multilabeled tree, lateral gene transfer, likelihood, phylogeny, reconstruction, statistical model.
Note: ArXiv version entitled The pattern and process of gene family evolution.
       
Toggle abstract
313
photo
Steven Kelk. A note on efficient computation of hybridization number via softwired clusters. 2011.
Keywords: explicit network, FPT, from clusters, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1108.4642.
       

314
photo
Paul Phipps. Planar phylogenetic network optimization. PhD thesis, University of Texas at Dallas, U.S.A., 2011.
Keywords: abstract network, from distances, phylogenetic network, Program PhippsNetwork, split, split network.
Note: http://proquest.umi.com/pqdlink?did=2337197411&Fmt=7&clientId=176295&RQT=309&VName=PQD.
       

315
photo
Puspal Bhabak. Improving the approximation ratio of the maximum agreement forest (MAF) on k trees and estimating the approximation ratio of the acyclic-MAF on k trees. Master's thesis, University of Windsor, Canada, 2011.
Keywords: agreement forest, approximation, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction.
Note: http://scholar.uwindsor.ca/cgi/viewcontent.cgi?article=1315&context=etd.
       

316
photophotophotophoto
Mukul S. Bansal, Guy Banay, J. Peter Gogarten and Ron Shamir. Detecting Highways of Horizontal Gene Transfer. In JCB, Vol. 18(9):1087-1114, 2011.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://people.csail.mit.edu/mukul/HighwayFull_preprint.pdf.
       
Toggle abstract
317
photo
Thu-Hien To. On some graph problems in phylogenetics. PhD thesis, Université Paris Diderot - Paris 7, France, 2011.
Keywords: explicit network, from triplets, level k phylogenetic network, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.liafa.jussieu.fr/~toth/thesis.pdf.
       

318
photo
Alethea Rea. Statistical approaches to phylogenetic networks, recombination and testing of incongruence. PhD thesis, The University of Auckland, New Zealand, 2011.
Keywords: abstract network, AIC, BIC, phylogenetic network, phylogeny, split, split network, statistical model.
Note: https://researchspace.auckland.ac.nz/handle/2292/67624.
       

319
photo
Rosalba Radice. A Bayesian Approach to Phylogenetic Networks. PhD thesis, University of Bath, U.K., 2011.
Keywords: bayesian, explicit network, from sequences, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://opus.bath.ac.uk/25521/.
       

320
photophotophotophoto
Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin and Vincent Berry. Models, algorithms and programs for phylogeny reconciliation. In Briefings in Bioinformatics, Vol. 12(5):392-400, 2011.
Keywords: explicit network, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
       
Toggle abstract
321
photophoto
Alix Boc and Vladimir Makarenkov. Towards an accurate identification of mosaic genes and partial horizontal gene transfers. In NAR, Vol. 39(21):e144, 2011.
Keywords: explicit network, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program T REX, reconstruction.
Note: http://dx.doi.org/10.1093/nar/gkr735.
       
Toggle abstract
322
photophoto
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.
       

323

Miro Ferreri, Weijie Qu and Bo Han. Phylogenetic networks: A tool to display character conflict and demographic history. In African Journal of Biotechnology , Vol. 10(60):12799-12803, 2011.
Keywords: phylogenetic network, phylogeny, survey, visualization.
       

324
photo
Benjamin Albrecht. Fast Computation of Hybridization Networks. Master's thesis, University of Tübingen, Germany, 2011.
Keywords: explicit network, from rooted trees, minimum number, phylogenetic network, phylogeny, reconstruction.
       

325
photophotophotophoto
Louxin Zhang, Yen Kaow Ng, Taoyang Wu and Yu Zheng. Network model and efficient method for detecting relative duplications or horizontal gene transfers. In ICCABS11, Pages 214-219, 2011.
Keywords: dynamic programming, explicit network, from network, from rooted trees, from species tree, phylogenetic network, phylogeny, polynomial, reconstruction.
       
Toggle abstract
326
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
327
photophoto
Zhi-Zhong Chen and Lusheng Wang. HybridNET: a tool for constructing hybridization networks. In BIO, Vol. 26(22):2912-2913, 2010.
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNET, software.
Note: http://rnc.r.dendai.ac.jp/~chen/papers/note2.pdf.
       
Toggle abstract
328
photo
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/.
       

329
photophotophoto
Changiz Eslahchi, Mahnaz Habibi, Reza Hassanzadeh and Ehsan Mottaghi. MC-Net: a method for the construction of phylogenetic networks based on the Monte-Carlo method. In BMCEB, Vol. 10:254, 2010.
Keywords: abstract network, circular split system, from distances, heuristic, phylogenetic network, Program MC-Net, Program SplitsTree, software, split, split network.
Note: http://dx.doi.org/10.1186/1471-2148-10-254.
       
Toggle abstract
330
photophotophotophoto
Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Path lengths in tree-child time consistent hybridization networks. In Information Sciences, Vol. 180(3):366-383, 2010.
Keywords: distance between networks, phylogenetic network, phylogeny, time consistent network, tree-child network.
Note: http://arxiv.org/abs/0807.0087?context=cs.CE.
       
Toggle abstract
331
photophoto
Johannes Fischer and Daniel H. Huson. New Common Ancestor Problems in Trees and Directed Acyclic Graphs. In IPL, Vol. 110(8-9):331-335, 2010.
Keywords: explicit network, phylogenetic network, polynomial.
Note: http://www-ab.informatik.uni-tuebingen.de/people/fischer/lsa.pdf.
       
Toggle abstract
332
photo
Stephen J. Willson. Regular Networks Can Be Uniquely Constructed from Their Trees. In TCBB, Vol. 8(3):785-796, 2010.
Keywords: explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, regular network.
Note: http://www.public.iastate.edu/~swillson/RegularNetsFromTrees5.pdf.
       
Toggle abstract
333
photo
Luay Nakhleh. Evolutionary phylogenetic networks: models and issues. In L. Heath and N. Ramakrishnan editors, The Problem Solving Handbook for Computational Biology and Bioinformatics, Springer, 2010.
Keywords: phylogenetic network, phylogeny, survey.
Note: http://www.cs.rice.edu/~nakhleh/Papers/HeathRamakrishnanBookChapter.pdf.
       

334
photophotophotophoto
Leo van Iersel, Steven Kelk, Regula Rupp and Daniel H. Huson. Phylogenetic Networks Do not Need to Be Complex: Using Fewer Reticulations to Represent Conflicting Clusters. In ISMB10, Vol. 26(12):i124-i131 of BIO, 2010.
Keywords: from clusters, level k phylogenetic network, Program Dendroscope, Program HybridInterleave, Program HybridNumber, reconstruction.
Note: http://dx.doi.org/10.1093/bioinformatics/btq202, with proofs: http://arxiv.org/abs/0910.3082.
       
Toggle abstract
335
photophoto
Joel Velasco and Elliott Sober. Testing for Treeness: Lateral Gene Transfer, Phylogenetic Inference, and Model Selection. In Biology and Philosophy, Vol. 25(4):675-687, 2010.
Keywords: explicit network, model selection, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://joelvelasco.net/Papers/velascosober-testingfortreeness.pdf.
       
Toggle abstract
336
photo
David A. Morrison. Using data-display networks for exploratory data analysis in phylogenetic studies. In MBE, Vol. 27(5):1044-1057, 2010.
Keywords: abstract network, hybridization, NeighborNet, Program SplitsTree, recombination, split decomposition.
Note: http://dx.doi.org/10.1093/molbev/msp309.
       
Toggle abstract
337
photophotophoto
Simone Linz, Charles Semple and Tanja Stadler. Analyzing and reconstructing reticulation networks under timing constraints. In JOMB, Vol. 61(5):715-737, 2010.
Keywords: explicit network, from rooted trees, hybridization, lateral gene transfer, NP complete, phylogenetic network, phylogeny, reconstruction, time consistent network.
Note: http://dx.doi.org/10.1007/s00285-009-0319-y..
       
Toggle abstract
338
photophotophoto
Alix Boc, Hervé Philippe and Vladimir Makarenkov. Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity. In Systematic Biology, Vol. 59(2):195-211, 2010.
Note: http://www.info2.uqam.ca/~makarenv/makarenv/Artcile_SB_2010.pdf.
       

339
photophotophotophotophoto
Tetsuo Asano, Jesper Jansson, Kunihiko Sadakane, Ryuhei Uehara and Gabriel Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. In CPM10, Vol. 6129:190-201 of LNCS, springer, 2010.
Keywords: distance between networks, explicit network, level k phylogenetic network, phylogenetic network, polynomial, spread.
Note: http://hdl.handle.net/10119/9859, slides available at http://cs.nyu.edu/parida/CPM2010/MainPage_files/18.pdf.
       
Toggle abstract
340
photophoto
Erik W. Bloomquist and Marc A. Suchard. Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework. In Systematic Biology, Vol. 59(1):27-41, 2010.
Note: http://dx.doi.org/10.1093/sysbio/syp076.
       

341
photo
Yufeng Wu. Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees. In ISMB10, Vol. 26(12):i140-i148 of BIO, 2010.
Keywords: explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program PIRN, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btq198.
       
Toggle abstract
342
photo
Yufeng Wu and Jiayin Wang. Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees. In ISBRA10, Vol. 6053:203-214 of LNCS, springer, 2010.
Keywords: agreement forest, explicit network, from rooted trees, hybridization, integer linear programming, minimum number, phylogenetic network, phylogeny, Program HybridNumber, Program SPRDist, SPR distance.
Note: http://www.engr.uconn.edu/~ywu/Papers/ISBRA10WuWang.pdf.
       
Toggle abstract
343
photo
Robert G. Beiko. Gene sharing and genome evolution: networks in trees and trees in networks. In Biology and Philosophy, Vol. 25(4):659-673, 2010.
Keywords: abstract network, explicit network, from rooted trees, galled network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, reconstruction, split network, survey.
Note: http://dx.doi.org/10.1007/s10539-010-9217-3.
       
Toggle abstract
344
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
345
photo
David A. Morrison. Phylogenetic networks in systematic biology (and elsewhere) In R.M. Mohan editor, Research Advances in Systematic Biology, Global Research Network, Trivandrum, India, 2010.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, reconstruction, survey.
       

346
photophotophoto
Hyun Jung Park, Guohua Jin and Luay Nakhleh. Bootstrap-based Support of HGT Inferred by Maximum Parsimony. In BMCEB, Vol. 10:131, 2010.
Keywords: bootstrap, explicit network, from sequences, lateral gene transfer, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2148-10-131.
       
Toggle abstract
347
photophotophoto
Leo van Iersel, Charles Semple and Mike Steel. Locating a tree in a phylogenetic network. In IPL, Vol. 110(23), 2010.
Keywords: cluster containment, explicit network, from network, level k phylogenetic network, normal network, NP complete, phylogenetic network, polynomial, regular network, time consistent network, tree containment, tree sibling network, tree-child network.
Note: http://arxiv.org/abs/1006.3122.
       
Toggle abstract
348
photophotophotophoto
Sophie Abby, Eric Tannier, Manolo Gouy and Vincent Daubin. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. In BMCB, Vol. 11:324, 2010.
Keywords: agreement forest, explicit network, from rooted trees, from species tree, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program EEEP, Program PhyloNet, Program Prunier, reconstruction, software.
Note: http://www.biomedcentral.com/1471-2105/11/324.
       
Toggle abstract
349
photophotophoto
Gabriel Cardona, Mercè Llabrés and Francesc Rosselló. A metric for galled networks. 2010.
Keywords: distance between networks, explicit network, from network, galled network, phylogenetic network, phylogeny.
Note: http://arxiv4.library.cornell.edu/abs/1009.0652.
       

350
photophotophoto
Chris Whidden, Robert G. Beiko and Norbert Zeh. Fast FPT Algorithms for Computing Rooted Agreement Forests: Theory and Experiments. In Proceedings of the ninth International Symposium on Experimental Algorithms (SEA'10), Vol. 6049:141-153 of LNCS, springer, 2010.
Keywords: agreement forest, explicit network, FPT, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, Program HybridInterleave, reconstruction, SPR distance.
Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2010-03.pdf.
       
Toggle abstract
351
photophotophoto
Fumei Lam, Ryan Tarpine and Sorin Istrail. The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy. In JCB, Vol. 17(6), 2010.
Keywords: explicit network, from sequences, heuristic, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.brown.edu/~sorin/pdfs/Lam%20the%20imperfect.pdf.
       

352
photophotophoto
Gabriel Cardona, Mercè Llabrés and Francesc Rosselló. Two Results on Distances for Phylogenetic Networks. In Advances in Intelligent and Soft Computing, Vol. 74:93-100, 2010.
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, tree sibling network.
Note: http://www.merilibrary.com/books/bioinformatics/advances%20in%20bioinformatics.pdf#page=103.
       

353
photo
Cuong Than. Inference of parsimonious species phylogenies from multi-locus data. PhD thesis, Rice University, U.S.A., 2010.
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://hdl.handle.net/1911/62177.
       

354
photophotophotophotophotophotophoto
Marta Melé, Asif Javed, Marc Pybus, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit and Genographic Consortium. A New Method to Reconstruct Recombination Events at a Genomic Scale. In PLoS Computational Biology, Vol. 6(11):e1001010.1-13, 2010.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1371/journal.pcbi.1001010.
       
Toggle abstract
355
photo
Binh T. Nguyen. Novel Split-Based Approaches to Computing Phylogenetic Diversity and Planar Split Networks. PhD thesis, University of East Anglia, U.K., 2010.
Keywords: abstract network, diversity, from splits, phylogenetic network, phylogeny, reconstruction, split, split network, visualization.
Note: https://ueaeprints.uea.ac.uk/id/eprint/34218.
       

356
photo
Pawel Górecki. H-trees: a model of evolutionary scenario with horizontal gene transfer. In Fundamenta Informaticae, Vol. 103:105-128, 2010.
Keywords: duplication, lateral gene transfer, loss, phylogenetic network, phylogeny, uniqueness.
       

357
photophotophoto
Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Comparison of tree-child phylogenetic networks. In TCBB, Vol. 6(4):552-569, 2009.
Keywords: explicit network, phylogenetic network, phylogeny, Program Bio PhyloNetwork, Program PhyloNetwork, tree sibling network, tree-child network.
Note: http://arxiv.org/abs/0708.3499.
       
Toggle abstract
358
photophotophoto
Stefan Grünewald, Vincent Moulton and Andreas Spillner. Consistency of the QNet algorithm for generating planar split networks from weighted quartets. In DAM, Vol. 157(10):2325-2334, 2009.
Keywords: abstract network, consistency, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software.
Note: http://dx.doi.org/10.1016/j.dam.2008.06.038.
       
Toggle abstract
359
photophoto
Ulrik Brandes and Sabine Cornelsen. Phylogenetic Graph Models Beyond Trees. In DAM, Vol. 157(10):2361-2369, 2009.
Keywords: abstract network, cactus graph, from splits, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.inf.uni-konstanz.de/~cornelse/Papers/bc-pgmbt-07.pdf.
       
Toggle abstract
360
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.
       

361
photo
Daniel H. Huson. Drawing Rooted Phylogenetic Networks. In TCBB, Vol. 6(1):103-109, 2009.
Keywords: explicit network, phylogenetic network, phylogeny, Program Dendroscope, Program SplitsTree, visualization.
Note: http://dx.doi.org/10.1109/TCBB.2008.58.
       
Toggle abstract
362
photophoto
Simone Linz and Charles Semple. Hybridization in non-binary trees. In TCBB, Vol. 6(1):30-45, 2009.
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, reconstruction.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/LS08.pdf, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw03/1220/linz/.
       

363
photophoto
Sagi Snir and Tamir Tuller. The NET-HMM approach: Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In JBCB, Vol. 7(4):625-644, 2009.
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://research.haifa.ac.il/~ssagi/published%20papers/Snir-NET-HMM-JBCB-2009.pdf.
       
Toggle abstract
364
photophotophotophotophoto
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.
       

365
photophotophotophoto
Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Metrics for phylogenetic networks I: Generalizations of the Robinson-Foulds metric. In TCBB, Vol. 6(1):46-61, 2009.
Keywords: distance between networks, explicit network, phylogenetic network, phylogeny, time consistent network, tree-child network, tripartition distance.
Note: http://dx.doi.org/10.1109/TCBB.2008.70.
       
Toggle abstract
366
photophotophotophoto
Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Metrics for phylogenetic networks II: Nodal and triplets metrics. In TCBB, Vol. 6(3):454-469, 2009.
Keywords: distance between networks, phylogenetic network, phylogeny.
Note: http://dx.doi.org/10.1109/TCBB.2008.127.
       
Toggle abstract
367
photophotophotophoto
Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. On Nakhleh's metric for reduced phylogenetic networks. In TCBB, Vol. 6(4):629-638, 2009.
Keywords: distance between networks, phylogenetic network, phylogeny.
Note: Preliminary versions: http://arxiv.org/abs/0809.0110 and http://arxiv.org/abs/0801.2354v1.
       
Toggle abstract
368
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic. In TCBB, Vol. 6(3):495-505, 2009.
Keywords: explicit network, heuristic, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb-MP.pdf.
       

369
photophotophoto
Luay Nakhleh, Derek Ruths and Hideki Innan. Gene Trees, Species Trees, and Species Networks. In R. Guerra, D. B. Allison and D. Goldstein editors, Meta-analysis and Combining Information in Genetics and Genomics, 2009.
Keywords: coalescent, explicit network, from rooted trees, from species tree, phylogenetic network, phylogeny, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/GuerraGoldsteinBookChapter.pdf.
       

370
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.
       

371
photophoto
Ran Libeskind-Hadas and Michael A. Charleston. On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem. In JCB, Vol. 16(1):105-117, 2009.
Keywords: cophylogeny, heuristic, NP complete, parsimony, phylogenetic network, reconstruction.
Note: http://dx.doi.org/10.1089/cmb.2008.0084.
       
Toggle abstract
372
photophoto
Thu-Hien To and Michel Habib. Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time. In CPM09, (5577):275-288, springer, 2009.
Keywords: explicit network, from triplets, level k phylogenetic network, minimum number, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/0901.1657.
       
Toggle abstract
373
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
374
photophotophotophotophoto
Daniel H. Huson, Regula Rupp, Vincent Berry, Philippe Gambette and Christophe Paul. Computing Galled Networks from Real Data. In ISMBECCB09, Vol. 25(12):i85-i93 of BIO, 2009.
Keywords: abstract network, cluster containment, explicit network, FPT, from clusters, from rooted trees, galled network, NP complete, phylogenetic network, phylogeny, polynomial, Program Dendroscope, reconstruction.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00368545/en/.
       
Toggle abstract
375
photophotophotophoto
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
376
photophoto
Peter J. Humphries and Charles Semple. Note on the hybridization number and subtree distance in phylogenetics. In Applied Mathematics Letters, Vol. 22(4):611-615, 2009.
Keywords: explicit network, minimum number, phylogenetic network, phylogeny, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/HS08.pdf.
       

377
photophotophotophotophotophoto
Laxmi Parida, Asif Javed, Marta Melé, Francesc Calafell, Jaume Bertranpetit and Genographic Consortium. Minimizing recombinations in consensus networks for phylogeographic studies. In BMCB, Vol. 10(Suppl 1):S72, 2009.
Note: Selected papers from the Seventh Asia-Pacific Bioinformatics Conference (APBC 2009), http://dx.doi.org/10.1186/1471-2105-10-S1-S72.
       
Toggle abstract
378
photophoto
Robert G. Beiko and Mark A. Ragan. Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction. In Horizontal Gene Transfer, Vol. 532:241-256 of Methods in Molecular Biology, 2009.
Note: http://dx.doi.org/10.1007/978-1-60327-853-9_14.
       
Toggle abstract
379
photo
Maria S. Poptsova. Testing Phylogenetic Methods to Identify Horizontal Gene Transfer. In Horizontal Gene Transfer, Pages 227-240, 2009.
Note: http://dx.doi.org/10.1007/978-1-60327-853-9_13.
       
Toggle abstract
380
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
381
photophoto
Sarah C. Ayling and Terence A. Brown. Novel methodology for construction and pruning of quasi-median networks. In BMCB, Vol. 9:115, 2009.
Keywords: abstract network, from sequences, median network, phylogenetic network, phylogeny, quasi-median network, reconstruction.
Note: http://dx.doi.org/10.1186/1471-2105-9-115.
       
Toggle abstract
382
photo
Martin Lott. New Methods for Constructing Phylogenetic Networks from Multi-Labelled Trees. PhD thesis, University of East Anglia, U.K., 2009.
Keywords: duplication, explicit network, from multilabeled tree, phylogenetic network, phylogeny, Program PADRE, reconstruction, software.
Note: http://www.ic0.net/thesis-martin-final.pdf.
       

383
photo
Klaus Schliep. Some applications of statistical phylogenetics. PhD thesis, Massey University, New Zealand, 2009.
Keywords: abstract network, phylogenetic network, Program Phangorn, reconstruction, split network.
Note: http://muir.massey.ac.nz/handle/10179/931.
       

384
photophotophotophotophotophoto
Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. Constructing Level-2 Phylogenetic Networks from Triplets. In TCBB, Vol. 6(4):667-681, 2009.
Note: http://www.win.tue.nl/~liersel/level2full.pdf.
       

385
photo
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.
       

386
photo
Mark A. Ragan. Trees and networks before and after Darwin. In Biology Direct, Vol. 4(43), 2009.
Keywords: abstract network, explicit network, phylogenetic network, phylogeny, survey, visualization.
Note: http://dx.doi.org/10.1186/1745-6150-4-43.
       
Toggle abstract
387
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.
       

388
photophotophotophotophotophoto
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
389
photo
Laura S. Kubatko. Identifying Hybridization Events in the Presence of Coalescence via Model Selection. In Systematic Biology, Vol. 58(5):478-488, 2009.
Keywords: AIC, BIC, branch length, coalescent, explicit network, from rooted trees, from species tree, hybridization, lineage sorting, model selection, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1093/sysbio/syp055.
       

390
photo
Chen Meng and Laura S. Kubatko. Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model. In Theoretical Population Biology, Vol. 75(1):35-45, 2009.
Keywords: bayesian, coalescent, from network, from rooted trees, hybridization, likelihood, lineage sorting, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1016/j.tpb.2008.10.004.
       
Toggle abstract
391
photophoto
Marc Thuillard and Didier Fraix-Burnet. Phylogenetic Applications of the Minimum Contradiction Approach on Continuous Characters. In Evolutionary Bioinformatics, Vol. 5:53-46, 2009.
Keywords: from continuous characters, minimum contradiction, phylogenetic network, phylogeny, split, split network.
Note: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747132/.
       

392
photophotophoto
Bui Quang Minh, Steffen Klaere and Arndt von Haeseler. Taxon Selection under Split Diversity. In Systematic Biology, Vol. 58(6):586-594, 2009.
Keywords: abstract network, circular split system, diversity, from network, phylogenetic network, split network.
Note: http://dx.doi.org/10.1093/sysbio/syp058.
       
Toggle abstract
393
photophotophotophoto
Bui Quang Minh, Fabio Pardi, Steffen Klaere and Arndt von Haeseler. Budgeted Phylogenetic Diversity on Circular Split Systems. In TCBB, Vol. 6(1):22-29, 2009.
Keywords: abstract network, circular split system, dynamic programming, from network, phylogenetic network, polynomial, split, split network.
Note: http://dx.doi.org/10.1109/TCBB.2008.54.
       
Toggle abstract
394
photo
Qiong Wu. Phylogenetic Networks: New Constructions and Applications. PhD thesis, Université of East Anglia, U.K., 2009.
Keywords: abstract network, phylogenetic network, phylogeny, reconstruction, split network.
Note: http://ethos.bl.uk/OrderDetails.do?did=1&uin=uk.bl.ethos.514315.
       

395

Poornima Venugopal. Improving layout of phylogenetic network produced by PADRE. Master's thesis, University of Texas at Dallas, U.S.A., 2009.
Keywords: explicit network, phylogenetic network, Program PADRE, visualization.
Note: http://proquest.umi.com/pqdlink?did=2026498501&sid=1&Fmt=2&clientId=176295&RQT=309&VName=PQD.
       

396
photo
Poornima Venugopal and Sergey Bereg. Layout of Phylogenetic Networks and Multi-Labeled Trees. In BIOT'09, Pages 91, 2009.
Keywords: explicit network, phylogenetic network, phylogeny, Program PADRE, visualization.
Note: http://www.biotconf.org/PDFs/1456.pdf.
       

397
photo
Chris Whidden. A Unifying View on Approximation and FPT of Agreement Forests. Master's thesis, Dalhousie University, Canada, 2009.
Keywords: agreement forest, approximation, explicit network, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://web.cs.dal.ca/~whidden/MCSThesis09.pdf.
       

398
photophoto
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.
       

399
photophoto
Chris Whidden and Norbert Zeh. A Unifying View on Approximation and FPT of Agreement Forests. In WABI09, Vol. 5724:390-402 of LNCS, Springer, 2009.
Keywords: agreement forest, approximation, explicit network, FPT, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: https://www.cs.dal.ca/sites/default/files/technical_reports/CS-2009-02.pdf.
       
Toggle abstract
400
photophotophoto
Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Tripartitions do not always discriminate phylogenetic networks. In MBIO, Vol. 211(2):356-370, 2008.
Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree-child network, tripartition distance.
Note: http://arxiv.org/abs/0707.2376, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0904/valiente/.
       
Toggle abstract
401
photophoto
Philippe Gambette and Daniel H. Huson. Improved Layout of Phylogenetic Networks. In TCBB, Vol. 5(3):472-479, 2008.
Keywords: abstract network, heuristic, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://hal-lirmm.ccsd.cnrs.fr/lirmm-00309694/en/.
       
Toggle abstract
402
photophotophoto
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
403
photophotophotophotophotophoto
Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen and Teun Boekhout. Constructing level-2 phylogenetic networks from triplets. In RECOMB08, Vol. 4955:450-462 of LNCS, springer, 2008.
Keywords: explicit network, from triplets, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, polynomial, Program Level2, reconstruction.
Note: http://homepages.cwi.nl/~iersel/level2full.pdf. An appendix with proofs can be found here http://arxiv.org/abs/0707.2890.
       
Toggle abstract
404
photophotophoto
Andreas Spillner, Binh T. Nguyen and Vincent Moulton. Computing phylogenetic diversity for split systems. In TCBB, Vol. 5(2):235-244, 2008.
Keywords: abstract network, diversity, phylogenetic network, phylogeny, split.
Note: http://dx.doi.org/10.1109/TCBB.2007.70260, slides available at http://www.newton.cam.ac.uk/webseminars/pg+ws/2007/plg/plgw01/0906/spillner/.
       
Toggle abstract
405
photophotophoto
Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. A Perl Package and an Alignment Tool for Phylogenetic Networks. In BMCB, Vol. 9:175, 2008.
Keywords: distance between networks, phylogenetic network, phylogeny, Program Bio PhyloNetwork, tree sibling network, tree-child network.
Note: http://dx.doi.org/10.1186/1471-2105-9-175.
       
Toggle abstract
406
photophotophotophoto
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
407
photophoto
Tobias Kloepper and Daniel H. Huson. Drawing explicit phylogenetic networks and their integration into SplitsTree. In BMCEB, Vol. 8(22), 2008.
Keywords: explicit network, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://dx.doi.org/10.1186/1471-2148-8-22.
       
Toggle abstract
408
photophotophotophoto
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi and Giancarlo Mauri. The Comparison of Phylogenetic Networks: Algorithms and Complexity. In Ion Mandoiu and Alexander Zelikovsky editors, Bioinformatics Algorithms, John Wiley and Sons Ltd, 2008.
Keywords: phylogenetic network, phylogeny.
Note: http://www.amazon.com/gp/reader/0470097736/.
       

409
photophotophoto
Steven M. Woolley, David Posada and Keith A. Crandall. A Comparison of Phylogenetic Network Methods Using Computer Simulation. In PLoS ONE, Vol. 3(4):e1913, 2008.
Keywords: abstract network, distance between networks, evaluation, median network, MedianJoining, minimum spanning network, NeighborNet, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program SHRUB, Program SplitsTree, Program TCS, split decomposition.
Note: http://dx.doi.org/10.1371/journal.pone.0001913.
       
Toggle abstract
410
photophotophotophoto
Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. A Distance Metric for a Class of Tree-Sibling Phylogenetic Networks. In BIO, Vol. 24(13):1481-1488, 2008.
Keywords: distance between networks, phylogenetic network, phylogeny, polynomial, tree sibling network.
Note: http://dx.doi.org/10.1093/bioinformatics/btn231.
       
Toggle abstract
411
photophotophotophoto
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.
       

412
photo
Simone Linz. Reticulation in evolution. PhD thesis, Heinrich-Heine-University, Düsseldorf, Germany, 2008.
Keywords: agreement forest, FPT, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, SPR distance, statistical model.
Note: http://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=8505.
       

413
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.
       

414
photophoto
Cuong Than and Luay Nakhleh. SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. In APBC08, Pages 251-260, 2008.
Keywords: evaluation, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/apbc08.pdf.
       

415
photophoto
Daniel H. Huson and Regula Rupp. Summarizing Multiple Gene Trees Using Cluster Networks. In WABI08, Vol. 5251:296-305 of LNCS, springer, 2008.
Keywords: abstract network, from clusters, from rooted trees, phylogenetic network, phylogeny, polynomial, Program Dendroscope.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_25, slides from the MIEP Conference available at http://www.lirmm.fr/MIEP08/slides/11_13_rupp.pdf.
       
Toggle abstract
416
photophoto
Lichen Bao and Sergey Bereg. Clustered SplitsNetworks. In COCOA08, Vol. 5165:469-478 of LNCS, springer, 2008.
Keywords: abstract network, from distances, NeighborNet, realization, reconstruction.
Note: http://dx.doi.org/10.1007/978-3-540-85097-7_44, slides available at http://www.utdallas.edu/~besp/cocoa08talk.pdf.
       
Toggle abstract
417
photo
Birgit Gemeinholzer. Phylogenetic networks. In Björn H. Junker and Falk Schreiber editors, Analysis of Biological Networks, Pages 255-282, John Wiley and Sons Ltd, 2008.
Keywords: survey.
Note: http://www.amazon.com/gp/reader/0470041447/.
       

418
photophoto
Sagi Snir and Tamir Tuller. Novel Phylogenetic Network Inference by Combining Maximum Likelihood and Hidden Markov Models. In WABI08, Vol. 5251:354-368 of LNCS, springer, 2008.
Keywords: explicit network, from sequences, HMM, lateral gene transfer, likelihood, phylogenetic network, phylogeny, statistical model.
Note: http://dx.doi.org/10.1007/978-3-540-87361-7_30.
       
Toggle abstract
419
photophotophotophoto
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.
       
Toggle abstract
420
photophotophotophoto
Gabriel Cardona, Mercè Llabrés, Francesc Rosselló and Gabriel Valiente. Phylogenetic Networks: Justification, Models, Distances and Algorithms. In VI Jornadas de Matemática Discreta y Algorítmica (JMDA'08), 2008.
Keywords: distance between networks, mu distance, phylogenetic network, phylogeny, polynomial, survey, time consistent network, tree-child network, tripartition distance, triplet distance.
Note: http://bioinfo.uib.es/media/uploaded/jmda2008_submission_61-1.pdf.
       

421
photophotophoto
Cuong Than, Derek Ruths and Luay Nakhleh. PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships. In BMCB, Vol. 9(322), 2008.
Keywords: Program PhyloNet, software.
Note: http://dx.doi.org/10.1186/1471-2105-9-322.
       
Toggle abstract
422
photophotophotophoto
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
423
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.
       

424
photophoto
Ernst Althaus and Rouven Naujoks. Reconstructing Phylogenetic Networks with One Recombination. In Proceedings of the seventh International Workshop on Experimental Algorithms (WEA'08), Vol. 5038:275-288 of LNCS, springer, 2008.
Keywords: enumeration, explicit network, exponential algorithm, from sequences, generation, parsimony, phylogenetic network, phylogeny, reconstruction, unicyclic network.
Note: http://dx.doi.org/10.1007/978-3-540-68552-4_21.
       
Toggle abstract
425
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
426
photophotophoto
Gabriel Cardona, Francesc Rosselló and Gabriel Valiente. Extended Newick: It is Time for a Standard Representation. In BMCB, Vol. 9:532, 2008.
Keywords: evaluation, explicit network, phylogenetic network, Program Bio PhyloNetwork, Program Dendroscope, Program NetGen, Program PhyloNet, Program SplitsTree, Program TCS, visualization.
Note: http://bioinfo.uib.es/media/uploaded/bmc-2008-enewick-sub.pdf.
       

427
photophoto
Supriya Munshaw and Thomas B. Kepler. An Information-Theoretic Method for the Treatment of Plural Ancestry in Phylogenetics. In MBE, Vol. 25(6):1199-1208, 2008.
Keywords: explicit network, from sequences, heuristic, phylogenetic network, reconstruction, simulated annealing, software.
Note: http://dx.doi.org/10.1093/molbev/msn066.
       
Toggle abstract
428
photophotophoto
Cuong Than, Guohua Jin and Luay Nakhleh. Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. In Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'08), Vol. 5267:113-127 of LNCS, springer, 2008.
Keywords: bootstrap, explicit network, from rooted trees, from sequences, lateral gene transfer, phylogenetic network, phylogeny, Program Nepal, Program PhyloNet, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg-08.pdf, slides available at http://igm.univ-mlv.fr/RCG08/RCG08slides/Cuong_Than_RCG08.pdf.
       

429
photo
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.
       

430
photophotophoto
Hadas Birin, Zohar Gal-Or, Isaac Elias and Tamir Tuller. Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion. In BIO, Vol. 24(6):826-832, 2008.
Note: http://dx.doi.org/10.1093/bioinformatics/btn024.
       
Toggle abstract
431
photophotophotophoto
Magnus Bordewich, Simone Linz, Katherine St. John and Charles Semple. A reduction algorithm for computing the hybridization number of two trees. In EBIO, Vol. 3:86-98, 2007.
Keywords: agreement forest, FPT, from rooted trees, hybridization, phylogenetic network, phylogeny, Program HybridNumber.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BLSS07.pdf.
       

432
photophoto
Magnus Bordewich and Charles Semple. Computing the minimum number of hybridization events for a consistent evolutionary history. In DAM, Vol. 155:914-918, 2007.
Keywords: agreement forest, approximation, APX hard, explicit network, from rooted trees, hybridization, inapproximability, NP complete, phylogenetic network, phylogeny, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS06a.pdf.
       

433
photophoto
Olivier Gauthier and François-Joseph Lapointe. Hybrids and Phylogenetics Revisited: A Statistical Test of Hybridization Using Quartets. In Systematic Botany, Vol. 32(1):8-15, 2007.
Keywords: explicit network, from quartets, hybridization, phylogenetic network, phylogeny, reconstruction, reticulogram, split decomposition.
Note: http://dx.doi.org/10.1600/036364407780360238.
       
Toggle abstract
434
photophoto
Olivier Gauthier and François-Joseph Lapointe. Seeing the Trees for the Network: Consensus, Information Content, and Superphylogenies. In Systematic Biology, Vol. 56(2):345-355, 2007.
Keywords: consensus.
Note: http://dx.doi.org/10.1080/10635150701286549.
       
Toggle abstract
435
photophotophotophoto
Stefan Grünewald, Kristoffer Forslund, Andreas W. M. Dress and Vincent Moulton. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. In MBE, Vol. 24(2):532-538, 2007.
Keywords: abstract network, circular split system, from quartets, phylogenetic network, phylogeny, Program QNet, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/24/2/532.
       
Toggle abstract
436
photophotophotophoto
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
437
photophotophotophoto
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
438
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.
       

439
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Efficient Parsimony-based Methods for Phylogenetic Network Reconstruction. In ECCB06, Vol. 23(2):e123-e128 of BIO, 2007.
Keywords: parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/eccb06.pdf.
       

440
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. In ISBRA07, Vol. 4463:61-72 of LNCS, springer, 2007.
Keywords: approximation, heuristic, parsimony, phylogenetic network, phylogeny, Program Nepal.
Note: http://www.cs.rice.edu/~nakhleh/Papers/isbra07.pdf.
       

441
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Inferring Phylogenetic Networks by the Maximum Parsimony Criterion: A Case Study. In MBE, Vol. 24(1):324-337, 2007.
Keywords: explicit network, parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/MBE06.pdf.
       

442
photophotophotophoto
Cam Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung and Louxin Zhang. Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. In TCBB, Vol. 4(3):394-402, 2007.
Keywords: explicit network, from sequences, labeling, NP complete, parsimony, phylogenetic network, phylogeny.
Note: http://www.cs.washington.edu/homes/ncthach/Papers/TCBB2007.pdf.
       

443
photo
Stephen J. Willson. Unique determination of some homoplasies at hybridization events. In BMB, Vol. 69(5):1709-1725, 2007.
Keywords: explicit network, from network, hybridization, labeling, normal network, phylogenetic network, tree-child network.
Note: http://www.public.iastate.edu/~swillson/unique.det.pdf.
       

444
photo
Stephen J. Willson. Reconstruction of Some Hybrid Phylogenetic Networks with Homoplasies from Distances. In BMB, Vol. 69(8):2561-2590, 2007.
Keywords: explicit network, from distances, normal network, phylogenetic network, phylogeny, reconstruction.
Note: http://www.public.iastate.edu/~swillson/BMB06-97.willson.pdf.
       

445
photophotophoto
David Bryant, Vincent Moulton and Andreas Spillner. Consistency of the Neighbor-Net Algorithm. In AMB, Vol. 2(8), 2007.
Keywords: abstract network, consistency, from distances, NeighborNet.
Note: http://dx.doi.org/10.1186/1748-7188-2-8.
       
Toggle abstract
446
photophoto
Maria S. Poptsova and J. Peter Gogarten. The power of phylogenetic approaches to detect horizontally transferred genes. In BMCEB, Vol. 7(45), 2007.
Keywords: evaluation, from rooted trees, lateral gene transfer, Program EEEP.
Note: http://dx.doi.org/10.1186/1471-2148-7-45.
       
Toggle abstract
447
photo
Monique M. Morin. Phylogenetic Networks: Simulation, Characterization, and Reconstruction. PhD thesis, The University of New Mexico, U.S.A., 2007.
Keywords: evaluation, explicit network, hybridization, lateral gene transfer, phylogenetic network, phylogeny, Program NetGen, simulation, software.
Note: http://www.cs.unm.edu/~morin/morin_phd.pdf.
       

448
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.
       

449
photophoto
Tamir Tuller and Sagi Snir. The NET-HMM: a HMM Based Likelihood Model for Evolutionary Networks. 2007.
Keywords: lateral gene transfer, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: Poster presented at the eleventh Annual International Conference on Research in Computational Molecular Biology (RECOMB'07), http://www.qb3.org/recomb07/posters/Tuller013043013RECOMB_HMM1.pdf.
       

450
photophoto
Patricia Buendia and Giri Narasimhan. Searching for Recombinant Donors in a Phylogenetic Network of Serial Samples. In ISBRA07, Vol. 4463:109-120 of LNCS, springer, 2007.
Keywords: evaluation, phylogenetic network, phylogeny, recombination, recombination detection.
Note: http://dx.doi.org/10.1007/978-3-540-72031-7_10.
       

451
photophoto
Patricia Buendia and Giri Narasimhan. Sliding MinPD: Building evolutionary networks of serial samples via an automated recombination detection approach. In BIO, Vol. 23(22):2993-3000, 2007.
Keywords: from sequences, phylogenetic network, phylogeny, Program Sliding MinPD, recombination, recombination detection, serial evolutionary networks, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btm413.
       
Toggle abstract
452
photophotophotophoto
Galina Glazko, Vladimir Makarenkov, Jing Liu and Arcady Mushegian. Evolutionary history of bacteriophages with double-stranded DNA genomes. In Biology Direct, Vol. 2(36), 2007.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, Program T REX.
Note: http://dx.doi.org/10.1186/1745-6150-2-36.
       
Toggle abstract
453
photophotophotophoto
Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. In JCB, Vol. 14(4):517-535, 2007.
Keywords: counting, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-jcb.pdf.
       

454
photo
Hans-Jürgen Bandelt and Arne Dür. Translating DNA data tables into quasi-median networks for parsimony analysis and error detection. In MPE, Vol. 42(1):256-271, 2007.
Keywords: abstract network, from sequences, parsimony, phylogenetic network, phylogeny, quasi-median network, reconstruction.
Note: http://dx.doi.org/10.1016/j.ympev.2006.07.013.
       
Toggle abstract
455
photo
Nicolas Galtier. A model of horizontal gene transfer and the bacterial phylogeny problem. In Systematic Biology, Vol. 56(4):633-642, 2007.
Keywords: explicit network, generation, lateral gene transfer, phylogenetic network, phylogeny, Program HGT_simul, software, statistical model.
Note: http://dx.doi.org/10.1080/10635150701546231.
       
Toggle abstract
456
photo
Yuanyi Zhang. Optimization Algorithms for Phylogenetic Networks. PhD thesis, University of Texas at Dallas, U.S.A., 2007.
Keywords: abstract network, explicit network, from distances, phylogenetic network, phylogeny, reconstruction, split, split network, visualization.
Note: http://proquest.umi.com/pqdlink?did=1421626541&sid=1&Fmt=6&clientId=176295&RQT=309&VName=PQD.
       

457
photophotophoto
Hadas Birin, Zohar Gal-Or, Isaac Elias and Tamir Tuller. Inferring Models of Rearrangements, Recombinations, and Horizontal Transfers by the Minimum Evolution Criterion. In WABI07, Vol. 4645:111-123 of LNCS, springer, 2007.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://safrabio.cs.tau.ac.il/download/Papers/Birin_et_al.pdf.
       

458
photo
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.
       

459
photophotophoto
Mihaela Baroni, Charles Semple and Mike Steel. Hybrids in Real Time. In Systematic Biology, Vol. 55(1):46-56, 2006.
Keywords: agreement forest, from rooted trees, phylogenetic network, phylogeny, polynomial, reconstruction, time consistent network.
Note: http://www.math.canterbury.ac.nz/~m.steel/Non_UC/files/research/hybrids.pdf.
       
Toggle abstract
460
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
461
photophotophoto
Barbara R. Holland, Lars S. Jermiin and Vincent Moulton. Improved Consensus Network Techniques for Genome-Scale Phylogeny. In Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005 (SMBE'05), Vol. 23(5):848-855 of MBE, 2006.
Keywords: consensus.
Note: http://dx.doi.org/10.1093/molbev/msj061.
       

462
photophoto
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
463
photophoto
Daniel H. Huson and David Bryant. Application of Phylogenetic Networks in Evolutionary Studies. In MBE, Vol. 23(2):254-267, 2006.
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, survey.
Note: http://dx.doi.org/10.1093/molbev/msj030, software available from www.splitstree.org.
       
Toggle abstract
464
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
465
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
466
photophotophotophoto
Guohua Jin, Luay Nakhleh, Sagi Snir and Tamir Tuller. Maximum Likelihood of Phylogenetic Networks. In BIO, Vol. 22(21):2604-2611, 2006.
Keywords: explicit network, likelihood, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/NetworksML06.pdf, supplementary material: http://www.cs.rice.edu/~nakhleh/Papers/Supp-ML.pdf.
       

467
photophotophoto
Vladimir Makarenkov, Dmytro Kevorkov and Pierre Legendre. Phylogenetic Network Construction Approaches. In Applied Mycology and Biotechnology, Vol. 6:61-97, 2006.
Keywords: from distances, hybridization, lateral gene transfer, median network, NeighborNet, netting, Program Arlequin, Program Network, Program Pyramids, Program Reticlad, Program SplitsTree, Program T REX, Program TCS, Program WeakHierarchies, pyramid, reticulogram, split, split decomposition, split network, survey, weak hierarchy.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/MKL_article.pdf.
       

468
photophoto
Monique M. Morin and Bernard M. E. Moret. NetGen: generating phylogenetic networks with diploid hybrids. In BIO, Vol. 22(15):1921-1923, 2006.
Keywords: generation, hybridization, Program NetGen, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btl191.
       
Toggle abstract
469
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.
       

470
photophotophotophoto
Cuong Than, Derek Ruths, Hideki Innan and Luay Nakhleh. Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. In Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'06), Vol. 4205:215-229 of LNCS, springer, 2006.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, Program LatTrans, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/recombcg06-final.pdf.
       

471
photo
Stephen J. Willson. Unique Reconstruction of Tree-Like Phylogenetic Networks from Distances Between Leaves. In BMB, Vol. 68:919-944, 2006.
Keywords: explicit network, from distances, identifiability, mrca network, phylogenetic network, phylogeny, reconstruction.
Note: http://www.public.iastate.edu/~swillson/BMB05-07.rev8.pdf.
       

472
photophoto
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.
       
Toggle abstract
473
photophoto
Patricia Buendia and Giri Narasimhan. Serial NetEvolve: A flexible utility for generating serially-sampled sequences along a tree or recombinant network. In BIO, Vol. 18(22):2313-2314, 2006.
Keywords: generation, phylogenetic network, phylogeny, Program Serial NetEvolve, Program Treevolve, recombination, software.
Note: http://dx.doi.org/10.1093/bioinformatics/btl387.
       
Toggle abstract
474
photophotophotophoto
Tetsuo Asano, Patricia Evans, Ryuhei Uehara and Gabriel Valiente. Site Consistency in Phylogenetic Networks with Recombination. In C. S. Iliopoulos, K. Park and K. Steinhöfel editors, Algorithms in Bioinformatics, Vol. 6:15-26 of Texts in Algorithmics, College Publications, 2006.
       

475
photo
Kim McBreen and Peter J. Lockhart. Reconstructing reticulate evolutionary histories of plants. In Trends in Plant Science, Vol. 11(8):103-122, 2006.
Note: http://www.aseanbiodiversity.info/Abstract/51006032.pdf.
       

476
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.
       

477
photo
Pawel Górecki. Detection of horizontal gene transfer. PhD thesis, Warsaw University, Poland, 2006.
Keywords: explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
       

478
photophoto
Mihaela Baroni and Mike Steel. Accumulation Phylogenies. In ACOM, Vol. 10(1):19-30, 2006.
Keywords: abstract network, from clusters, from distances, phylogenetic network, phylogeny, polynomial, reconstruction, regular network.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.137.1960.
       
Toggle abstract
479
photophoto
Sergey Bereg and Kathryn Bean. Constructing Phylogenetic Networks from Trees. In BIBE05, Pages 299-305, 2005.
Keywords: evaluation, from distances, phylogenetic network, phylogeny, Program SplitsTree, Program T REX, reconstruction, split, split network.
Note: http://dx.doi.org/10.1109/BIBE.2005.19.
       
Toggle abstract
480
photophotophotophoto
Mihaela Baroni, Stefan Grünewald, Vincent Moulton and Charles Semple. Bounding the number of hybridization events for a consistent evolutionary history. In JOMB, Vol. 51(2):171-182, 2005.
Keywords: agreement forest, bound, explicit network, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BGMS05.pdf.
       
Toggle abstract
481
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
482
photo
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.
       

483
photophoto
Dan Gusfield and Vikas Bansal. A Fundamental Decomposition Theory for Phylogenetic Networks and Incompatible Characters. In RECOMB05, Vol. 3500:217-232 of LNCS, springer, 2005.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, polynomial, recombination, reconstruction.
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/gusfieldrecomb.pdf.
       

484
photophotophoto
Barbara R. Holland, Frédéric Delsuc and Vincent Moulton. Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods. In Systematic Biology, Vol. 54(1):66-76, 2005.
Keywords: consensus.
Note: http://hal-sde.archives-ouvertes.fr/halsde-00193050/fr/.
       
Toggle abstract
485
photophoto
Daniel H. Huson and Tobias Kloepper. Computing recombination networks from binary sequences. In ECCB05, Vol. 21(suppl. 2):ii159-ii165 of BIO, 2005.
Keywords: from sequences, phylogenetic network, phylogeny, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1126.
       
Toggle abstract
486
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.
       

487
photophotophotophoto
Victor Kunin, Leon Goldovsky, Nikos Darzentas and Christos A. Ouzounis. The net of life: Reconstructing the microbial phylogenetic network. In GR, Vol. 15:954-959, 2005.
Note: http://dx.doi.org/10.1101/gr.3666505.
       
Toggle abstract
488
photophotophotophoto
Martyn Kennedy, Barbara R. Holland, Russel D. Gray and Hamish G. Spencer. Untangling Long Branches: Identifying Conflicting Phylogenetic Signals Using Spectral Analysis, Neighbor-Net, and Consensus Networks. In Systematic Biology, Vol. 54(4):620-633, 2005.
Keywords: abstract network, consensus, NeighborNet, phylogenetic network, phylogeny.
Note: http://awcmee.massey.ac.nz/people/bholland/pdf/Kennedy_etal_2005.pdf.
       

489
photo
David A. Morrison. Networks in phylogenetic analysis: new tools for population biology. In IJP, Vol. 35:567-582, 2005.
Keywords: median network, NeighborNet, phylogenetic network, phylogeny, population genetics, Program Network, Program Spectronet, Program SplitsTree, Program T REX, Program TCS, reconstruction, reticulogram, split decomposition, survey.
Note: http://hem.fyristorg.com/acacia/papers/networks.pdf.
       

490
photophotophotophoto
Luay Nakhleh, Guohua Jin, Fengmei Zhao and John Mellor-Crummey. Reconstructing Phylogenetic Networks Using Maximum Parsimony. In CSB05, Pages 93-102, 2005.
Keywords: parsimony, phylogenetic network, phylogeny, Program Nepal, reconstruction.
Note: http://www.cs.rice.edu/~nakhleh/Papers/CSB05.pdf.
       

491
photophotophoto
Luay Nakhleh, Derek Ruths and Li-San Wang. RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. In COCOON05, Vol. 3595:84-93 of LNCS, springer, 2005.
Keywords: from rooted trees, heuristic, lateral gene transfer, phylogenetic network, phylogeny, Program PhyloNet.
Note: http://www.cs.rice.edu/~nakhleh/Papers/COCOON05.pdf.
       

492
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.
       

493
photophoto
Derek Ruths and Luay Nakhleh. Recombination and phylogeny: effects and detection. In IJBRA, Pages 202-212, 2005.
Note: http://www.cs.rice.edu/~nakhleh/Papers/IJBRA05.pdf.
       

494
photophotophoto
Yun S. Song, Yufeng Wu and Dan Gusfield. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. In ISMB05, Vol. 21:i413-i422 of BIO, 2005.
Keywords: integer linear programming, minimum number, Program HapBound, Program SHRUB, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1033.
       
Toggle abstract
495
photophotophotophotophoto
Richard C. Winkworth, David Bryant, Peter J. Lockhart, David Havell and Vincent Moulton. Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths. In Systematic Biology, Vol. 54(1):56-65, 2005.
Keywords: abstract network, from distances, from network, phylogenetic network, phylogeny, reconstruction, split, split network.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/05Biogeographic.pdf.
       

496
photophotophotophoto
Dave MacLeod, Robert L. Charlebois, W. Ford Doolittle and Eric Bapteste. Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement. In BMCEB, Vol. 5(27), 2005.
Keywords: explicit network, from rooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HorizStory, reconstruction, software.
Note: http://dx.doi.org/10.1186/1471-2148-5-27.
       
Toggle abstract
497
photophotophoto
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.
       

498
photo
David Bryant. Extending tree models to splits networks. In Lior Pachter and Bernd Sturmfels editors, Algebraic Statistics for Computational Biology, Pages 322-334, Cambridge University Press, 2005.
Keywords: abstract network, from splits, likelihood, phylogenetic network, phylogeny, split, split network, statistical model.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/05ascbChapter.pdf.
       

499
photo
Derek Ruths. Applications of phylogenetic incongruence to detecting and reconstructing interspecific recombination and horizontal gene transfer. Master's thesis, Rice University, U.S.A., 2005.
Keywords: explicit network, from rooted trees, from species tree, heuristic, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://hdl.handle.net/1911/17912.
       

500
photo
Wei-Shun Su, Tso-Ching Lee and Yaw-Ling Lin. Efficient Algorithms for Constructing Phylogenetic Networks with Restricted Recombinations. In NCS05, Pages 1-7, 2005.
Keywords: explicit network, from sequences, phylogenetic network, phylogeny, reconstruction.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.168.6735.
       

501
photophotophoto
Mihaela Baroni, Charles Semple and Mike Steel. A framework for representing reticulate evolution. In ACOM, Vol. 8:398-401, 2004.
Keywords: explicit network, from clusters, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction, regular network, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BSS04.pdf.
       
Toggle abstract
502
photophoto
Andreas W. M. Dress and Daniel H. Huson. Constructing splits graphs. In TCBB, Vol. 1(3):109-115, 2004.
Keywords: abstract network, circular split system, from trees, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network, visualization.
Note: http://scilib.kiev.ua/ieee/tcbb/2004/03/n3/n0109.pdf.
       
Toggle abstract
503
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
504
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
505
photophotophotophoto
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.
       
Toggle abstract
506
photophotophotophotophoto
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
507
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.
       

508
photophoto
C. Randal Linder and Loren H. Rieseberg. Reconstructing patterns of reticulate evolution in plants. In American Journal of Botany, Vol. 91(10):1700-1708, 2004.
Keywords: distance between networks, hybridization, phylogenetic network, phylogeny, reconstruction, survey, tripartition distance.
Note: http://www.amjbot.org/cgi/reprint/91/10/1700.pdf.
       

509
photophoto
Vladimir Makarenkov and Pierre Legendre. From a phylogenetic tree to a reticulated network. In JCB, Vol. 11(1):195-212, 2004.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program T REX, reticulogram.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/article_JCB2004.pdf.
       

510
photophotophoto
Vladimir Makarenkov, Pierre Legendre and Yves Desdevises. Modeling phylogenetic relationships using reticulated networks. In Zoologica Scripta, Vol. 33(1):89-96, 2004.
Note: http://www.labunix.uqam.ca/~makarenv/articles/ZoologicaScripta.pdf.
       

511
photophotophotophotophotophotophotophoto
Bernard M. E. Moret, Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun and Ruth Timme. Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. In TCBB, Vol. 1(1):13-23, 2004.
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, time consistent network, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/tcbb04.pdf.
       

512
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.
       

513
photophotophoto
Mike Hallett, Jens Lagergren and Ali Tofigh. Simultaneous Identification of Duplications and Lateral Transfers. In RECOMB04, Pages 347-356, 2004.
Keywords: duplication, explicit network, FPT, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.nada.kth.se/~jensl/p164-hallett.pdf.
       

514
photophotophotophoto
C. Randal Linder, Bernard M. E. Moret, Luay Nakhleh and Tandy Warnow. Network (Reticulate) Evolution: Biology, Models, and Algorithms. In PSB04, 2004.
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb04.pdf.
       

515
photophotophoto
Mohd Abdul Hai Zahid, Ankush Mittal and Ramesh C. Joshi. Use of Phylogenetic network and its reconstruction Algorithms. In Bioinformatics India, Vol. 2:47-58, 2004.
Keywords: evaluation, from distances, NeighborNet, Program SplitsTree, Program T REX, split decomposition.
Note: http://www.isical.ac.in/~zahid_t/publications/papers/1.pdf.
       

516
photo
Pawel Górecki. Reconciliation problems for duplication, loss and horizontal gene transfer. In RECOMB04, Pages 316-325, 2004.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://ai.stanford.edu/~serafim/CS374_2004/Papers/Gorecki_Reconciliation.pdf.
       

517
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.
       

518
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.
       

519
photophotophotophotophotophoto
Luay Nakhleh, Jerry Sun, Tandy Warnow, C. Randal Linder, Bernard M. E. Moret and Anna Tholse. Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. In PSB03, 2003.
Keywords: distance between networks, evaluation, phylogenetic network, phylogeny, polynomial, tripartition distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/psb03.pdf.
       

520
photo
Daniel H. Huson. What If I Don't Have a Tree? Split Decomposition and Related Models. In Current Protocols in Bioinformatics, Vol. Unit 6.7, 2003.
Keywords: abstract network, phylogenetic network, Program SplitsTree, software, split decomposition, split network.
Note: http://dx.doi.org/10.1002/0471250953.bi0607s01.
       

521
photo
Pawel Górecki. Single step reconciliation algorithm for duplication, loss and horizontal gene transfer model. In ECCB03, 2003.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, NP complete, parsimony, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://www.inra.fr/eccb2003/posters/pdf/short/S_gorecki.ps.
       

522

Vassily A. Lyubetsky and Vladimir V. V´yugin. Methods of horizontal gene transfer determination using phylogenetic data. In In Silico Biology, Vol. 3(1-2):17-31, 2003.
Note: http://www.bioinfo.de/isb/2003030003/.
       

523
photophoto
David Bryant and Vincent Moulton. Neighbor-Net: An Agglomerative Method for the Construction of Planar Phylogenetic Networks. In WABI02, Vol. 2452:375-391 of LNCS, springer, 2002.
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://dx.doi.org/10.1007/3-540-45784-4_28.
       

524
photophoto
Olivier Gauthier and François-Joseph Lapointe. A comparison of alternative methods for detecting reticulation events in phylogenetic analysis. In IFCS02, Pages 365-369, springer, 2002.
       

525
photophoto
Pierre Legendre and Vladimir Makarenkov. Reconstruction of biogeographic and evolutionary networks using reticulograms. In Systematic Biology, Vol. 51(2):199-216, 2002.
Keywords: phylogenetic network, phylogeny, reconstruction, reticulogram.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/Article_SB.pdf.
       

526
photophotophoto
David Posada, Keith A. Crandall and Edward C. Holmes. Recombination in Evolutionary Genomics. In ARG, Vol. 36:75-97, 2002.
Keywords: phylogenetic network, phylogeny, recombination, recombination detection, survey.
Note: http://dx.doi.org/10.1146/annurev.genet.36.040202.111115.
       
Toggle abstract
527
photophotophotophoto
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
528
photo
Vladimir Makarenkov. T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks. In BIO, Vol. 17(7):664-668, 2001.
Keywords: phylogenetic network, phylogeny, Program T REX, reconstruction, reticulogram, software, visualization.
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/Article_BIO.pdf.
       

529
photophoto
David Posada and Keith A. Crandall. Intraspecific gene genealogies: trees grafting into networks. In TEE, Vol. 16(1):37-45, 2001.
Keywords: likelihood, median network, netting, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program SplitsTree, Program T REX, Program TCS, pyramid, reticulogram, split decomposition, statistical parsimony, survey.
Note: http://darwin.uvigo.es/download/papers/09.networks01.pdf.
       

530
photophotophoto
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.
       

531

Mark T. Holder, Jennifer A. Anderson and Alisha K. Holloway. Difficulties in Detecting Hybridization. In Systematic Biology, Vol. 50(6):978-982, 2001.
Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1080/106351501753462911.
       
Toggle abstract
532
photophotophoto
Mark Clement, David Posada and Keith A. Crandall. TCS: a computer program to estimate gene genealogies. In MOLE, Vol. 9:1657-1659, 2000.
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, reconstruction, software, statistical parsimony.
Note: http://darwin.uvigo.es/download/papers/08.tcs00.pdf.
       
Toggle abstract
533
photo
François-Joseph Lapointe. How to account for reticulation events in phylogenetic analysis: A review of distance-based methods. In Journal of Classification, Vol. 17:175-184, 2000.
Keywords: abstract network, evaluation, from distances, phylogenetic network, Program Pyramids, Program SplitsTree, Program T REX, pyramid, reconstruction, reticulogram, split network, survey, weak hierarchy.
Note: http://dx.doi.org/10.1007/s003570000016.
       

534
photo
Pierre Legendre. Reticulate evolution: From bacteria to philosophers. In JCLA, Vol. 17:153-157, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.
       

535
photo
Pierre Legendre. Biological Applications of Reticulate Analysis. In JCLA, Vol. 17:191-195, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.
       

536
photo
F. James Rohlf. Phylogenetic models and reticulations. In JCLA, Vol. 17:185-189, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.
       

537
photo
Peter E. Smouse. Reticulation inside the species boundary. In JCLA, Vol. 17:165-173, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.
       

538
photo
Peter H. A. Sneath. Reticulate Evolution in Bacteria and Other Organisms: How Can We Study It? In JCLA, Vol. 17:360-368, 2000.
Note: http://www.bio.umontreal.ca/legendre/reprints/Special_Section.pdf.
       

539
photophotophoto
Alan R. Templeton, Keith A. Crandall and Charles F. Sing. A Cladistic Analysis of Phenotypic Associations With Haplotypes Inferred From Restriction Endonuclease Mapping and DNA Sequence Data. III. Cladogram Estimation. In GEN, Vol. 132:619-633, 2000.
Keywords: from sequences, parsimony, phylogenetic network, phylogeny, Program TCS, recombination, reconstruction, statistical parsimony.
Note: http://www.genetics.org/cgi/content/abstract/132/2/619.
       

540
photophoto
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
541
photophoto
Pierre Legendre and Vladimir Makarenkov. Improving the additive tree representation of a dissimilarity matrix using reticulations. In IFCS00, Pages 35-40, springer, 2000.
Keywords: phylogenetic network, phylogeny, reconstruction, reticulogram.
Note: http://www.info2.uqam.ca/~makarenv/makarenv/Article_IFCS.pdf.
       

542
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
543
photophoto
Tao Sang and Yang Zhong. Testing Hybridization Hypotheses Based on Incongruent Gene Trees. In Systematic Biology, Vol. 49(3):422-434, 2000.
Keywords: bootstrap, from rooted trees, hybridization, lateral gene transfer, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1080/10635159950127321.
       

544
photophotophotophoto
Jean-Christophe Aude, Yolande Diaz-Lazcoz, Jean-Jacques Codani and Jean-Loup Risler. Applications of the Pyramidal Clustering Method to Biological Objects. In CC, Vol. 23(3-4):303-315, 1999.
Keywords: from distances, phylogenetic network, phylogeny, Program Pyramids, pyramid, reconstruction, software, visualization.
Note: http://dx.doi.org/10.1016/S0097-8485(99)00006-6.
       

545
photo
W. Ford Doolittle. Phylogenetic Classification and the Universal Tree. In Science, Vol. 284:2124-2128, 1999.
Note: http://cas.bellarmine.edu/tietjen/Ecology/phylogenetic_classification_and_.htm.
       
Toggle abstract
546
photo
Nicholas C. Grassly and Andrew Rambaut. Treevolve, a program to simulate the evolution of DNA sequences under different population dynamic scenarios. 1999.
Keywords: generation, phylogenetic network, phylogeny, population genetics, Program Treevolve, software.
Note: http://evolve.zoo.ox.ac.uk/software/treevolve/manual.php.
       

547
photophoto
Vincent Berry and David Bryant. Faster reliable phylogenetic analysis. In RECOMB99, Pages 59-68, 1999.
Keywords: abstract network, from quartets, phylogenetic network, phylogeny, polynomial, Program SplitsTree, reconstruction, split network, weakly compatible.
Note: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.95.9151.
       

548
photo
Daniel H. Huson. SplitsTree: analyzing and visualizing evolutionary data. In BIO, Vol. 14(1):68-73, 1998.
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, software, split network.
Note: http://bioweb.pasteur.fr/docs/doc-gensoft/splitstree/splitstree.ps.
       

549
photophoto
Roderic D.M. Page and Michael A. Charleston. Trees within trees: phylogeny and historical associations. In TEE, Vol. 13(9):356-359, 1998.
Keywords: duplication, explicit network, from rooted trees, from species tree, lateral gene transfer, phylogenetic network, phylogeny, reconstruction, survey.
Note: http://taxonomy.zoology.gla.ac.uk/rod/papers/tree.pdf.
       

550
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.
       

551
photophotophotophoto
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.
       

552
photo
Wayne P. Maddison. Gene Trees in Species Trees. In Systematic Biology, Vol. 46(3):523-536, 1997.
Keywords: from rooted trees, from species tree, lateral gene transfer, phylogeny, reconstruction, time consistent network.
Note: http://dx.doi.org/10.2307/2413694.
       

553
photophotophoto
Andreas W. M. Dress, Daniel H. Huson and Vincent Moulton. Analyzing and visualizing distance data using SplitsTree. In DAM, Vol. 71(1):95-109, 1996.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, Program SplitsTree, software, split network, visualization.
Note: http://bibiserv.techfak.uni-bielefeld.de/splits/splits.pdf.
       

554
photo
Rainer Wetzel. Zur Visualisierung abstrakter Ahnlichkeitsbeziehungen. PhD thesis, Universität Bielefeld, Germany, 1995.
Keywords: abstract network, circular split system, visualization.
       

555
photophoto
Daniel H. Huson and Rainer Wetzel. Analyzing and visualizing sequence and distance data with SplitsTree V1.0.2. 1995.
Keywords: abstract network, phylogenetic network, phylogeny, Program SplitsTree, reconstruction, software, split network, visualization.
Note: Technical report, http://citeseer.ist.psu.edu/173442.html.
       

556
photo
Loren H. Rieseberg and James D. Morefield. Character expression, phylogenetic reconstruction, and the detection of reticulate evolution. In P. C. Hoch and A. G. Stephenson editors, Experimental and molecular approaches to plant biosystematics, Pages 333–353, 1995.
Keywords: hybridization, phylogeny, Program Reticlad.
Note: http://www3.botany.ubc.ca/rieseberglab/loren pubs/1995 Chapter in Experimental and Molecular approaches to Plant Biosystematics.pdf.
       

557

Zdenek Skála and Jan Zrzavý. Phylogenetic reticulations and cladistics: discussion of methodological concepts. In Cladistics, Vol. 10(3):305-313, 1994.
Keywords: explicit network, from rooted trees, from species tree, parsimony, phylogeny.
Note: http://dx.doi.org/10.1111/j.1096-0031.1994.tb00180.x.
       

558
photophotophoto
Joaquin Dopazo, Andreas W. M. Dress and Arndt von Haeseler. Split decomposition: a new technique to analyse viral evolution. In PNAS, Vol. 90:10320-10324, 1993.
Keywords: abstract network, phylogenetic network, phylogeny, split, split decomposition, split network, visualization.
Note: http://dx.doi.org/10.1073/pnas.90.21.10320.
       

559
photophoto
Arndt von Haeseler and Gary A. Churchill. Network models for sequence evolution. In JME, Vol. 37(1):77-85, 1993.
Keywords: explicit network, likelihood, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://dx.doi.org/10.1007/BF00170465.
       

560
photo
Jotun Hein. A heuristic method to reconstruct the history of sequences subject to recombination. In JME, Vol. 36(4):396-405, 1993.
Keywords: explicit network, from sequences, heuristic, parsimony, phylogenetic network, phylogeny, Program RecPars, recombination, recombination detection, software.
Note: http://dx.doi.org/10.1007/BF00182187.
       

561
photophoto
Hans-Jürgen Bandelt and Andreas W. M. Dress. A canonical decomposition theory for metrics on a finite set. In Advances in Mathematics, Vol. 92(1):47-105, 1992.
Keywords: abstract network, circular split system, from distances, split, split decomposition, split network, weak hierarchy, weakly compatible.
       
Toggle abstract
562
photophoto
Hans-Jürgen Bandelt and Andreas W. M. Dress. Split Decomposition: A new and useful approach to phylogenetic analysis of distance data. In MPE, Vol. 1(3):242-252, 1992.
Keywords: abstract network, from distances, phylogenetic network, phylogeny, reconstruction, split, split decomposition, split network.
Note: http://dx.doi.org/10.1016/1055-7903(92)90021-8.
       
Toggle abstract
563
photo
Lucinda A. McDade. Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic analysis. In Evolution, Vol. 46(5):1329-1346, 1992.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
Note: http://www.jstor.org/stable/2409940.
       

564
photo
Jotun Hein. Reconstructing evolution of sequences subject to recombination using parsimony. In MBIO, Vol. 98(2):185-200, 1990.
Note: http://dx.doi.org/10.1016/0025-5564(90)90123-G.
       
Toggle abstract
565
photophoto
Hans-Jürgen Bandelt and Andreas W. M. Dress. Weak hierarchies associated with similarity measures: an additive clustering technique. In BMB, Vol. 51:113-166, 1989.
Keywords: abstract network, clustering, from distances, from trees, phylogenetic network, phylogeny, Program WeakHierarchies, reconstruction, weak hierarchy.
Note: http://dx.doi.org/10.1007/BF02458841.
       
Toggle abstract
566
photo
Patrice Bertrand. Étude de la représentation pyramidale. PhD thesis, Université de Paris-Dauphine, France, 1986.
Keywords: abstract network, pyramid.
       

567

Victoria A. Funk. Phylogenetic patterns and hybridization. In Annals of the Missouri Botanical Garden, Vol. 72(4):681-715, 1985.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
Note: http://www.jstor.org/stable/2399220.
       

568
photo
Richard R. Hudson. Properties of the neutral allele model with intragenic recombination. In TPP, Vol. 23:183-201, 1983.
Keywords: coalescent.
Note: http://dx.doi.org/10.1016/0040-5809(83)90013-8, see also http://www.brics.dk/~compbio/coalescent/hudson_animator.html.
       
Toggle abstract
569
photo
Gareth J. Nelson. Reticulation in Cladograms. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 105-111, Columbia University Press, 1983.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
       

570
photo
Hans-Erik Wanntorp. Reticulated cladograms and the identification of hybrid taxa. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 81-88, Columbia University Press, 1983.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
       

571
photo
Christopher J. Humphries. Primary data in hybrid analysis. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 89-103, Columbia University Press, 1983.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
       

572
photo
Warren H. Wagner. Reticulistics: the recognition of hybrids and their role in cladistics and classification. In Advances in Cladistics: Proceedings of the Second meeting of the Willi Hennig Society (HENNIG II), Pages 63-79, 1983.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
       

573
photophoto
Kare Bremer and Hans-Erik Wanntorp. Hierarchy and reticulation in systematics. In Systematic Zoology, Vol. 28(4):624-627, 1979.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
Note: http://dx.doi.org/10.2307/2412572.
       

574
photo
Peter H. A. Sneath. Cladistic Representation of Reticulate Evolution. In Systematic Zoology, Vol. 24(3):165-173, 1975.
Keywords: explicit network, from rooted trees, from species tree, hybridization, parsimony, phylogeny.
Note: http://dx.doi.org/10.2307/2412721.