Semple Publications of Charles Semple     Order by:   Type | Year
Associated keywords
Article (Journal)
1
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Charles Semple. Size of a phylogenetic network. In DAM, Vol. 217(2):362-367, 2017.  
Keywords: compressed network, Number of vertices, phylogenetic network, phylogeny.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S16.pdf.
       

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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.
       

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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, SPR distance.
Note: https://simonelinz.files.wordpress.com/2017/04/bls171.pdf.
       

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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.
       

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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.
       

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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 child network, tree-based network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S15.pdf.
       

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Magnus Bordewich and Charles Semple. Determining phylogenetic networks from inter-taxa distances. In JOMB, Vol. 73(2):283-303, 2016.  
Keywords: from distances, phylogenetic network, phylogeny, reconstruction, reticulation-visible network, time consistent network, tree child network, uniqueness.
Note: http://132.181.26.35/~c.semple/papers/BS15b.pdf.
       

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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.
       

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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.
       
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10
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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.
       
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11
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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.
       

12
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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, 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.
       
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13
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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.
       
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14
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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.
       
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15
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Leo van Iersel, Charles Semple and Mike Steel. Quantifying the Extent of Lateral Gene Transfer Required to Avert a 'Genome of Eden'. In BMB, Vol. 72:1783–1798, 2010.  
Note: http://www.win.tue.nl/~liersel/LGT.pdf.
       
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16
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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..
       
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17
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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 child network, tree containment, tree sibling network.
Note: http://arxiv.org/abs/1006.3122.
       
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18
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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/.
       

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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.
       

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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.
       

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Magnus Bordewich and Charles Semple. Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable. In TCBB, Vol. 4(3):458-466, 2007.  
Keywords: FPT, hybridization.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS06b.pdf.
       

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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.
       

23
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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.
       

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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.
       
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25
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Charles Semple and Mike Steel. Unicyclic networks: compatibility and enumeration. In TCBB, Vol. 3(1):84-91, 2006.  
Keywords: enumeration, explicit network, galled tree, unicyclic network.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/SS06.pdf.
       

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Magnus Bordewich and Charles Semple. On the computational complexity of the rooted subtree prune and regraft distance. In ACOM, Vol. 8:409-423, 2005.  
Keywords: agreement forest, from rooted trees, NP complete, SPR distance.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/BS04.pdf.
       
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27
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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.
       
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28
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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.
       
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29
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Katharina Huber, Vincent Moulton and Charles Semple. Replacing cliques by stars in quasi-median graphs. In DAM, Vol. 143(1-3), 2004.  
Note: http://dx.doi.org/10.1016/j.dam.2004.03.002.
       
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InBook
30
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Charles Semple. Hybridization Networks. In Olivier Gascuel and Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 277-314, Oxford University Press, 2007.  
Keywords: hybridization, phylogenetic network, phylogeny, recombination.
Note: http://www.math.canterbury.ac.nz/~c.semple/papers/S06.pdf.
       

Misc
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Andrew R. Francis, Charles Semple and Mike Steel. New Characterisations of Tree-Based Networks and Proximity Measures. 2016.  
Keywords: characterization, explicit network, phylogenetic network, phylogeny, time consistent network, tree-based network.
Note: https://arxiv.org/abs/1611.04225.