Publications list            
Showing 1 - 30 (677 total)
1
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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.
       

2
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Leo van Iersel, Mark Jones and Celine Scornavacca. Improved maximum parsimony models for phylogenetic networks. In SB, 2018.  
Keywords: explicit network, from sequences, parsimony, phylogenetic network, phylogeny, reconstruction.
Note: To appear.
       

3
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Mathias Weller. Linear-Time Tree Containment in Phylogenetic Networks. 2017.  
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.
       

4
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Hussein A. Hejase, Natalie VandePol, Gregory A. Bonito and Kevin J. Liu. FastNet: Fast and accurate inference of phylogenetic networks using large-scale genomic sequence data. 2017.  
Keywords: explicit network, from rooted trees, heuristic, phylogenetic network, phylogeny, Program FastNet, reconstruction.
Note: http://biorxiv.org/content/early/2017/05/01/132795.
       

5
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Andrew R. Francis, Katharina Huber and Vincent Moulton. Tree-based unrooted phylogenetic networks. 2017.  
Keywords: characterization, explicit network, NP complete, phylogenetic network, phylogeny, tree-based network.
Note: https://arxiv.org/abs/1704.02062.
       

6
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Andreas Gunawan. Solving Tree Containment Problem for Reticulation-visible Networks with Optimal Running Time. 2017.  
Keywords: explicit network, from network, from rooted trees, phylogenetic network, phylogeny, polynomial, reticulation-visible network, tree containment.
Note: https://arxiv.org/abs/1702.04088.
       

7
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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. 2017.  
Keywords: APX hard, from network, from sequences, likelihood, NP complete, parsimony.
Note: https://arxiv.org/abs/1707.03648.
       

8
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Remie Janssen, Mark Jones, Péter L. Erdös, Leo van Iersel and Celine Scornavacca. Exploring the tiers of rooted phylogenetic network space using tail moves. 2017.  
Keywords: explicit network, from network, phylogenetic network, phylogeny, SPR distance.
Note: https://arxiv.org/abs/1708.07656.
       

9
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Joan Carles Pons, Charles Semple and Mike Steel. Nonbinary tree-based networks: characterisations, metrics, and support trees. 2017.  
Keywords: characterization, explicit network, from network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1710.07836.
       

10
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Jonathan Klawitter. The SNPR neighbourhood of tree-child networks. 2017.  
Keywords: distance between networks, phylogenetic network, phylogeny, SPR distance, tree child network.
Note: https://arxiv.org/abs/1707.09579
       

11
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Sarah Bastkowski, Daniel Mapleson, Andreas Spillner, Taoyang Wu, Monika Balvociute and Vincent Moulton. SPECTRE: a Suite of PhylogEnetiC Tools for Reticulate Evolution. 2017.  
Keywords: abstract network, NeighborNet, phylogenetic network, phylogeny, Program FlatNJ, Program QNet, Program SplitsTree, reconstruction, software, split network.
Note: https://doi.org/10.1101/169177.
       

12
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Sebastien Roch and Kun-Chieh Wang. Circular Networks from Distorted Metrics. 2017.  
Keywords: abstract network, circular split system, from distances, NeighborNet, phylogenetic network, phylogeny, reconstruction, split network.
Note: https://arxiv.org/abs/1707.05722.
       

13
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Paul Bastide, Claudia Solís-Lemus, Ricardo Kriebel, Kenneth William Sparks and Cécile Ané. Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations. 2017.  
Keywords: Ancestral trait reconstruction, from network, Program PhyloNetworks SNaQ, software, statistical model, statistical test.
Note: https://doi.org/10.1101/194050.
       

14
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Katharina Huber, Vincent Moulton, Charles Semple and Taoyang Wu. Quarnet inference rules for level-1 networks. 2017.  
Keywords: explicit network, From quarnets, galled tree, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction.
Note: https://arxiv.org/abs/1711.06720.
       

15
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Leo van Iersel and Vincent Moulton. Leaf-reconstructibility of phylogenetic networks. 2017.  
Keywords: from network, level k phylogenetic network, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: https://arxiv.org/abs/1701.08982.
       

16
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Kristina Wicke and Mareike Fischer. Phylogenetic diversity and biodiversity indices on phylogenetic networks. 2017.  
Keywords: diversity, explicit network, from network, normal network, phylogenetic network, phylogeny.
Note: https://arxiv.org/abs/1706.05279.
       

17
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Magnus Bordewich and Charles Semple. A universal tree-based network with the minimum number of reticulations. 2017.  
Keywords: explicit network, phylogenetic network, phylogeny, tree-based network.
Note: https://arxiv.org/abs/1707.08274.
       

18
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Simone Linz and Charles Semple. Attaching leaves and picking cherries to characterise the hybridisation number for a set of phylogenies. 2017.  
Keywords: agreement forest, explicit network, from rooted trees, phylogenetic network, phylogeny, reconstruction, tree child network.
Note: https://arxiv.org/abs/1712.04131.
       

19
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Magnus Bordewich, Katharina Huber, Vincent Moulton and Charles Semple. Recovering tree-child networks from shortest inter-taxa distance information. 2017.  
Keywords: explicit network, from distances, phylogenetic network, phylogeny, reconstruction, tree child network.
Note: https://arxiv.org/abs/1711.08866.
       

20
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Andrew R. Francis and Vincent Moulton. Identifiability of tree-child phylogenetic networks under a probabilistic recombination-mutation model of evolution. 2017.  
Keywords: explicit network, from unrooted trees, phylogenetic network, phylogeny, tree child network, uniqueness.
Note: https://arxiv.org/abs/1712.04223.
       

21
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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.
       

22
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Jesper Jansson, Ramesh Rajaby and Wing-Kin Sung. An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees. In AlCoB17, Vol. 10252:115-126 of LNCS, Springer, 2017.  
Keywords: distance between networks, from network, phylogenetic network, phylogeny, polynomial, reconstruction, triplet distance.
Note: .
       

23
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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.
       

24
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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.
       

25
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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 trinets, NP complete, phylogenetic network, phylogeny, polynomial, reconstruction.
Note: http://arxiv.org/abs/1411.6804.
       

26
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Leo van Iersel, Steven Kelk, Giorgios Stamoulis, Leen Stougie and Olivier Boes. On unrooted and root-uncertain variants of several well-known phylogenetic network problems. In ALG, 2017.  
Keywords: explicit network, FPT, from network, from unrooted trees, NP complete, phylogenetic network, phylogeny, reconstruction, tree containment.
Note: https://hal.inria.fr/hal-01599716, to appear.
       

27
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Magnus Bordewich, Charles Semple and Nihan Tokac. Constructing tree-child networks from distance matrices. In Algorithmica, 2017.  
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, to appear.
       

28

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.
       

29
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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.
       

30
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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, galled tree, level k phylogenetic network, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://dx.doi.org/10.1007/s11538-017-0275-4.