Publications related to 'statistical model' : A statistical model aims at explaining how sequences evolve along the branches of a phylogenetic tree or network.
 
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2016
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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, phylogenetic network, phylogeny, statistical model, tree-based network.
Note: http://arxiv.org/abs/1606.07350.
       

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Jonathan Mitchell. Distinguishing Convergence on Phylogenetic Networks. PhD thesis, University of Tasmania, Australia, 2016.  
Keywords: phylogenetic network, phylogeny, statistical model.
Note: http://arxiv.org/abs/1606.07160.
       

2015
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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.
       

2013
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Sha Zhu. Stochastic tree models and probabilistic modelling of gene trees of given species networks. PhD thesis, University of Canterbury, New Zealand, 2013.  
Keywords: from network, generation, phylogenetic network, phylogeny, simulation, statistical model.
Note: http://hdl.handle.net/10092/7944.
       

2012
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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.
       
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Simon Joly. JML: Testing hybridization from species trees. In Molecular Ecology Ressources, Vol. 12(1):179-184, 2012.  
Keywords: from species tree, hybridization, lineage sorting, phylogenetic network, phylogeny, Program JML, statistical model.
Note: http://www.plantevolution.org/pdf/JMLpaper_accepted.pdf.
       
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Rosalba Radice. A Bayesian Approach to Modelling Reticulation Events with Application to the Ribosomal Protein Gene rps11 of Flowering Plants. In Australian & New Zealand Journal of Statistics, Vol. 54(4):401-426, 2012.  
Keywords: bayesian, phylogenetic network, phylogeny, reconstruction, statistical model.
       
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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.
       
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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.
       

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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.
       
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2011
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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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Sha Zhu, James H. Degnan and Mike Steel. Probabilistic modeling of gene trees given species networks. 2011.  
Keywords: from network, generation, phylogenetic network, phylogeny, statistical model.
Note: Poster, http://www.newton.ac.uk/programmes/PLG/Zhu.pdf.
       

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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.
       
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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.
       

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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/.
       

2010
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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.
       
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2009
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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.
       
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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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Simon Joly, Patricia A. McLenachan and Peter J. Lockhart. A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting. In The American Naturalist, Vol. 174(2):E54-E70, 2009.  
Keywords: hybridization, lineage sorting, phylogenetic network, phylogeny, reconstruction, statistical model.
Note: http://www.plantevolution.org/pdf/Joly&al_2009_AmNat.pdf.
       
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2008
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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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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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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.
       
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2007
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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.
       

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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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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.
       
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2005
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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.
       

2004
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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.
       

2001
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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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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.
       
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2000
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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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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.
       

1996
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Paul Marjoram and Robert C. Griffiths. Ancestral inference from samples of DNA sequences with recombination. In JCB, Vol. 3(4):479-502, 1996.  
Keywords: ARG, phylogenetic network, phylogeny, statistical model.
Note: http://www.math.canterbury.ac.nz/~r.sainudiin/recomb/JCB_paper.pdf.
       

1993
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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.