Search results for ' MBE ' :
    149 matches found.
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.
       

2
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Philippe Gambette, Katharina Huber and Steven Kelk. On the challenge of reconstructing level-1 phylogenetic networks from triplets and clusters. In JOMB, Vol. 74(7):1729-1751, 2017.  
Keywords: galled tree, phylogenetic network, phylogeny, reconstruction, uniqueness.
Note: http://dx.doi.org/10.1007/s00285-016-1068-3.
       

3
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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.
       

4
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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.
       

5
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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.
       

6
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Andrew R. Francis, Katharina Huber, Vincent Moulton and Taoyang Wu. Bounds for phylogenetic network space metrics. 2017.  
Keywords: bound, distance between networks, from network, NNI distance, SPR distance, TBR distance.
Note: https://arxiv.org/abs/1702.05609.
       

7
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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.
       

8
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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: .
       

9
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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, 2017.  
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/, to appear.
       

10
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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, phylogenetic network, phylogeny, SPR distance.
Note: https://hal-upec-upem.archives-ouvertes.fr/hal-01572624/en/.
       

11
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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.
       

12
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Claudia Solís-Lemus, Paul Bastide and Cécile Ané. PhyloNetworks: A Package for Phylogenetic Networks. In MBE, 2017.  
Keywords: from sequences, from trees, likelihood, Program PhyloNetworks SNaQ, software.
Note: https://doi.org/10.1093/molbev/msx235, to appear.
       

13
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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
       

14
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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.
       

15
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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.
       

16
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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.
       

17
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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 .
       

18
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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.
       

19
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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.
       

20
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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 trinets, galled tree, phylogenetic network, phylogeny, Program LEV1ATHAN, Program TriLoNet, reconstruction.
       

21
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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.
       

22
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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.
       

23
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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.
       

24
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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.
       

25
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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.
       

26
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Leo van Iersel, Steven Kelk, Nela Lekic and Leen Stougie. Approximation algorithms for nonbinary agreement forests. In SIDMA, Vol. 28(1):49-66, 2014.  
Keywords: agreement forest, approximation, from rooted trees, hybridization, minimum number, phylogenetic network, phylogeny, reconstruction.
Note: http://arxiv.org/abs/1210.3211.
       
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27
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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.
       
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28
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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.
       

29
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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.
       
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30
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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.
       

31
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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.
       

32
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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.
       

33
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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.
       

34
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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.
       
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35
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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.
       
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36
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Teresa Piovesan and Steven Kelk. A simple fixed parameter tractable algorithm for computing the hybridization number of two (not necessarily binary) trees. In TCBB, Vol. 10(1):18-25, 2013.  
Keywords: FPT, from rooted trees, phylogenetic network, phylogeny, Program TerminusEst, reconstruction.
Note: http://arxiv.org/abs/1207.6090.
       
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37
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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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38
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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.
       
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39
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Hoa Vu, Francis Chin, Wing-Kai Hon, Henry Leung, Kunihiko Sadakane, Wing-Kin Sung and Siu-Ming Yiu. Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees. In ISBRA13, Vol. 7875:112-124 of LNCS, springer, 2013.  
Keywords: from rooted trees, k-reticulated, phylogenetic network, phylogeny, polynomial, Program ARTNET, Program CMPT, reconstruction.
Note: http://grid.cs.gsu.edu/~xguo9/publications/2013_Cloud%20computing%20for%20de%20novo%20metagenomic%20sequence%20assembly.pdf#page=123.
       
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40
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Mukul S. Bansal, Guy Banay, Timothy J. Harlow, J. Peter Gogarten and Ron Shamir. Systematic inference of highways of horizontal gene transfer in prokaryotes. In BIO, Vol. 29(5):571-579, 2013.  
Keywords: duplication, explicit network, from species tree, from unrooted trees, lateral gene transfer, phylogenetic network, phylogeny, Program HiDe, Program RANGER-DTL, reconstruction.
Note: http://people.csail.mit.edu/mukul/Bansal_Highways_Bioinformatics_2013.pdf.
       

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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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42
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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.
       

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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.
       

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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/.
       
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45
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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.
       

46
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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.
       

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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.
       
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48
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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.
       
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49
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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.
       
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50
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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.
       
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51
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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, phylogenetic network, phylogeny, polynomial, reconstruction, split, split network.
Note: http://hal.archives-ouvertes.fr/hal-00678046/en/.
       
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52
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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.
       
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53
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Reza Hassanzadeh, Changiz Eslahchi and Wing-Kin Sung. Constructing phylogenetic supernetworks based on simulated annealing. In MPE, Vol. 63(3):738-744, 2012.  
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, software, split network.
Note: http://dx.doi.org/10.1016/j.ympev.2012.02.009.
       
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54
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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.
       
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55
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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.
       
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56
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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.
       

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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.
       
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58
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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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59
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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.
       
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60
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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.
       
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61
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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.
       

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Lavanya Kannan, Hua Li and Arcady Mushegian. A Polynomial-Time Algorithm Computing Lower and Upper Bounds of the Rooted Subtree Prune and Regraft Distance. In JCB, Vol. 18(5):743-757, 2011.  
Keywords: bound, minimum number, polynomial, SPR distance.
Note: http://dx.doi.org/10.1089/cmb.2010.0045.
       
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63
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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.
       
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64
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Lawrence A. David and Eric J. Alm. Rapid evolutionary innovation during an Archaean genetic expansion. In Nature, Vol. 469:93-96, 2011.  
Keywords: duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, parsimony, phylogenetic network, phylogeny, Program Angst.
Note: http://dx.doi.org/10.1038/nature09649, Program Angst described here.
       

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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.
       

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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.
       
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67
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Changiz Eslahchi and Reza Hassanzadeh. New Algorithm for Constructing Supernetworks from Partial Trees. In MCCMB11, Pages 106-107, 2011.  
Keywords: abstract network, from unrooted trees, heuristic, phylogenetic network, phylogeny, Program SNSA, reconstruction, simulated annealing, split network.
Note: http://mccmb.belozersky.msu.ru/2011/mccmb11.pdf#page=106.
       

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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.
       

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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.
       
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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/.
       

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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.
       
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72
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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.
       
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73
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Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola and Lusheng Wang. Beyond evolutionary trees. In Natural Computing, Vol. 9(2):421-435, 2010.  
Note: http://dx.doi.org/10.1007/s11047-009-9156-6.
       
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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.
       
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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.
       
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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.
       
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77
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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: 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.
       
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78
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Hyun Jung Park, Guohua Jin and Luay Nakhleh. Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees. In CSB10, 2010.  
Keywords: bound, from rooted trees, heuristic, phylogenetic network, phylogeny, reconstruction, SPR distance.
Note: http://www.cs.rice.edu/~nakhleh/Papers/ParkEtAl-CSB2010.pdf.
       

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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.
       
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80
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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.
       

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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.
       

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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.
       
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83
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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/.
       
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84
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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/.
       
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85
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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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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.
       

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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.
       
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Ali Tofigh. Using Trees to Capture Reticulate Evolution, Lateral Gene Transfers and Cancer Progression. PhD thesis, KTH Royal Institute of Technology, Sweden, 2009.  
Keywords: duplication, dynamic programming, from multilabeled tree, from rooted trees, from species tree, lateral gene transfer, loss, NP complete, phylogenetic network, phylogeny, reconstruction.
Note: http://kth.diva-portal.org/smash/record.jsf?pid=diva2:220830&searchId=1.
       

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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.
       

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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.
       
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91
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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.
       

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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.
       
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93
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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/.
       
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94
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Rune Lyngsø, Yun S. Song and Jotun Hein. Accurate Computation of Likelihoods in the Coalescent with Recombination via Parsimony. In RECOMB08, Vol. 4955:463-477 of LNCS, springer, 2008.  
Keywords: coalescent, likelihood, phylogenetic network, phylogeny, recombination, statistical model.
Note: http://dx.doi.org/10.1007/978-3-540-78839-3_41.
       
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95
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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.
       
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96
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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.
       

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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.
       

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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.
       

99
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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.
       

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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 child network, tree sibling network.
Note: http://dx.doi.org/10.1093/molbev/msn219.
       
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101
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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.
       
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102
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Miguel Arenas and David Posada. Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography. In BMCB, Vol. 8(458), 2008.  
Keywords: coalescent, generation, Program Recodon, software.
Note: http://dx.doi.org/10.1186/1471-2105-8-458.
       
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103
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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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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.
       

105
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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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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.
       
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107
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Dan Gusfield, Dean Hickerson and Satish Eddhu. An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study. In DAM, Vol. 155(6-7):806-830, 2007.  
Note: http://wwwcsif.cs.ucdavis.edu/~gusfield/cclowerbound.pdf.
       
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108
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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.
       
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109
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Daniel H. Huson. Split networks and Reticulate Networks. In Olivier Gascuel and Mike Steel editors, Reconstructing Evolution, New Mathematical and Computational Advances, Pages 247-276, Oxford University Press, 2007.  
Keywords: abstract network, consensus, from rooted trees, from sequences, from splits, from unrooted trees, galled tree, hybridization, phylogenetic network, phylogeny, Program Beagle, Program Spectronet, Program SplitsTree, Program SPNet, recombination, reconstruction, split network, survey.
Note: similar to http://www-ab.informatik.uni-tuebingen.de/research/phylonets/GCB2006.pdf.
       

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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.
       

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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.
       
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112
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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.
       

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Joanna L. Davies, Frantisek Simancík, Rune Lyngsø, Thomas Mailund and Jotun Hein. On Recombination-Induced Multiple and Simultaneous Coalescent Events. In GEN, Vol. 177:2151-2160, 2007.  
Keywords: coalescent, phylogenetic network, phylogeny, recombination, statistical model.
Note: http://dx.doi.org/10.1534/genetics.107.071126.
       
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114
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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.
       

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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.
       
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116
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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.
       

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Robert G. Beiko and Nicholas Hamilton. Phylogenetic identification of lateral genetic transfer events. In BMCEB, Vol. 6(15), 2006.  
Keywords: evaluation, from rooted trees, from unrooted trees, lateral gene transfer, Program EEEP, Program HorizStory, Program LatTrans, reconstruction, software, SPR distance.
Note: http://dx.doi.org/10.1186/1471-2148-6-15.
       
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118
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Olivier Gauthier. Utilisation de réseaux en analyse phylogénétique. PhD thesis, Université de Montréal, Canada, 2006.  
Note: http://igm.univ-mlv.fr/phylnet/PhylogeneticNetworks/docs/GauthierPhdThesis.pdf.
       

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Vineet Bafna and Vikas Bansal. Improved recombination lower bounds for haplotype data. In RECOMB05, Vol. 3500:569-584 of LNCS, springer, 2005.  
Keywords: bound, minimum number, phylogeny, recombination.
Note: http://www.cse.ucsd.edu/users/vbafna/pub/recomblb05.pdf.
       

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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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121
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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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122
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Trinh N. D. Huynh, Jesper Jansson, Nguyen Bao Nguyen and Wing-Kin Sung. Constructing a Smallest Refining Galled Phylogenetic Network. In RECOMB05, Vol. 3500:265-280 of LNCS, springer, 2005.  
Keywords: from rooted trees, galled tree, NP complete, phylogenetic network, phylogeny, polynomial, Program SPNet, reconstruction.
Note: http://www.df.lth.se/~jj/Publications/refining_gn3_RECOMB2005.pdf.
       

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Rune Lyngsø, Yun S. Song and Jotun Hein. Minimum Recombination Histories by Branch and Bound. In WABI05, Vol. 3692:239-250 of LNCS, springer, 2005.  
Keywords: ARG, branch and bound, from sequences, minimum number, Program Beagle, recombination, reconstruction, software.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/WABI05-239.pdf.
       

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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.
       

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Yun S. Song and Jotun Hein. Constructing Minimal Ancestral Recombination Graphs. In JCB, Vol. 12(2):147-169, 2005.  
Keywords: ARG, minimum number, recombination.
Note: http://www.eecs.berkeley.edu/~yss/Pub/SH-JCB05.pdf.
       

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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: minimum number, Program HapBound, Program SHRUB, recombination.
Note: http://dx.doi.org/10.1093/bioinformatics/bti1033.
       
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127
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Insa Cassens, Patrick Mardulyn and Michel C. Milinkovitch. Evaluating Intraspecific Network Construction Methods Using Simulated Sequence Data: Do Existing Algorithms Outperform the Global Maximum Parsimony Approach? In Systematic Biology, Vol. 54(3):363-372, 2005.  
Keywords: abstract network, evaluation, from unrooted trees, haplotype network, parsimony, phylogenetic network, phylogeny, Program Arlequin, Program CombineTrees, Program Network, Program TCS, reconstruction, software.
Note: http://www.lanevol.org/LANE/publications_files/Cassens_etal_SystBio_2005.pdf.
       

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Vineet Bafna and Vikas Bansal. The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds. In TCBB, Vol. 1(2):78-90, 2004.  
Keywords: ARG, bound, minimum number, phylogeny, recombination.
Note: http://www-cse.ucsd.edu/users/vbafna/pub/tcbb04.pdf.
       
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129
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David Bryant and Vincent Moulton. NeighborNet: An Agglomerative Method for the Construction of Phylogenetic Networks. In MBE, Vol. 21(2):255-265, 2004.  
Keywords: phylogenetic network, phylogeny, Program SplitsTree, reconstruction, split network.
Note: http://www.math.auckland.ac.nz/~bryant/Papers/04NeighborNet.pdf.
       
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130
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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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131
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Dan Gusfield and Dean Hickerson. A Fundamental, Efficiently-Computed Lower Bound on the Number of Recombinations Needed in Phylogenetic Networks. 2004.  
Note: UC Davis Computer Science Technical Report.
       

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Barbara R. Holland, Katharina Huber, Vincent Moulton and Peter J. Lockhart. Using consensus networks to visualize contradictory evidence for species phylogeny. In MBE, Vol. 21(7):1459-1461, 2004.  
Keywords: consensus, from trees, phylogenetic network, phylogeny, split, visualization.
Note: http://dx.doi.org/10.1093/molbev/msh145.
       
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Luay Nakhleh. Phylogenetic Networks. PhD thesis, University of Texas at Austin, U.S.A., 2004.  
Keywords: distance between networks, evaluation, generation, phylogenetic network, phylogeny, Program SPNet, reconstruction, split, statistical model, tree sibling network.
Note: http://www.library.utexas.edu/etd/d/2004/nakhlehl042/nakhlehl042.pdf.
       

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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.
       

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Yun S. Song and Jotun Hein. On the Minimum Number of Recombination Events in the Evolutionary History of DNA Sequences. In JOMB, Vol. 48(2):160-186, 2004.  
Keywords: minimum number, recombination.
Note: http://dx.doi.org/10.1007/s00285-003-0227-5.
       
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136
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Alix Boc, Vladimir Makarenkov and Abdoulaye B. Diallo. Une nouvelle méthode pour la détection de transferts horizontaux de gène : la réconciliation topologique d'arbres de gène et d'espèces. In JOBIM04, 2004.  
Note: http://www.labunix.uqam.ca/~makarenv/makarenv/JOBIM_2004.pdf.
       

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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.
       

138
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Simon R. Myers and Robert C. Griffiths. Bounds on the Minimum Number of Recombination Events in a Sample History. In GEN, Vol. 163:375-394, 2003.  
Keywords: Program RecMin.
Note: http://www.genetics.org/cgi/content/abstract/163/1/375.
       

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Yun S. Song and Jotun Hein. Parsimonious reconstruction of sequence evolution and haplotype blocks: Finding the minimum number of recombination events. In WABI03, Vol. 2812:287-302 of LNCS, springer, 2003.  
Keywords: minimum number, recombination.
Note: http://www.cs.ucdavis.edu/~yssong/Pub/SH-WABI03.pdf.
       

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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.
       

141
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Korbinian Strimmer, Carsten Wiuf and Vincent Moulton. Recombination Analysis Using Directed Graphical Models. In MBE, Vol. 18(1):97-99, 2001.  
Keywords: recombination, statistical model.
Note: http://mbe.oxfordjournals.org/cgi/content/full/18/1/97.
       

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Mikkel H. Schierup and Jotun Hein. Recombination and the molecular clock. In MBE, Vol. 17(10):1578-1579, 2000.  
Note: http://www.birc.dk/Publications/Articles/Schierup_2000c.pdf.
       

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Korbinian Strimmer and Vincent Moulton. Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models. In MBE, Vol. 17(6):875-881, 2000.  
Keywords: bayesian, likelihood, median network, split network, statistical model.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/17/6/875.
       

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Shizhong Xu. Phylogenetic Analysis Under Reticulate Evolution. In MBE, Vol. 17(6):897-907, 2000.  
Keywords: from distances, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/17/6/897.
       

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Hans-Jürgen Bandelt, Peter Forster and Arne Röhl. Median-joining networks for inferring intraspecies phylogenies. In MBE, Vol. 16(1):37-48, 1999.  
Keywords: from sequences, median network, MedianJoining, Program Network, reconstruction, software.
Note: http://mbe.oxfordjournals.org/cgi/content/abstract/16/1/37.
       

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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.
       

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Laurent Excoffier and Peter E. Smouse. Using Allele Frequencies and Geographic Subdivision to Reconstruct Gene Trees Within a Species: Molecular Variance Parsimony. In GEN, Vol. 136:343-359, 1994.  
Keywords: from distances, minimum spanning network, phylogenetic network, phylogeny, Program Arlequin, reconstruction, software.
Note: http://www.genetics.org/cgi/content/abstract/136/1/343.
       

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Richard R. Hudson and Norman L. Kaplan. Statistical Properties of the Number of Recombination Events in the History of a Sample of DNA Sequences. In GEN, Vol. 111:147-164, 1985.  
Note: http://www.genetics.org/cgi/content/abstract/111/1/147.
       

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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.
       
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