Inferring evolutionary scenarios in the duplication, loss and horizontal gene transfer model
作者： Paweł Górecki , Jerzy Tiuryn
DOI: 10.1007/978-3-642-29485-3_7
关键词: Horizontal gene transfer 、 Speciation 、 Computer science 、 Bioinformatics 、 Gene 、 Genetic algorithm 、 Gene duplication 、 Phylogenetic tree 、 Phylogenetics 、 Empirical data 、 Computational biology
摘要: An H-tree is a formal model of evolutionary scenario. It can be used to represent any processes with gene duplication and loss, horizontal transfer (HGT) speciation events. The H-trees, introduced in [26], an extension the duplication-loss (DL-model). Similarly its ancestor, it has number interesting mathematical biological properties. is, however, more computationally complex than DL-model. In this paper, we primarily address problem inferring H-trees that are compatible given tree phylogeny species HGTs. These results create computational foundation for general practical HGTs from trees We also demonstrate how our support HGT hypotheses based on empirical data sets.
springer.com
springerlink.com参考文章(56)
Maria Boekels Gogarten, J Peter Gogarten, Lorraine Olendzenski, None, Horizontal gene transfer : genomes in flux Humana Press. ,(2009)
Feifeng Zheng, Stanley P. Y. Fung, Wun-Tat Chan, Francis Y. L. Chin, Chung Keung Poon, Prudence W. H. Wong, Improved on-line broadcast scheduling with deadlines computing and combinatorics conference. pp. 320- 329 ,(2006) , 10.1007/11809678_34
J. Peter Gogarten, Ron Shamir, Mukul S. Bansal, Detecting highways of horizontal gene transfer research in computational molecular biology. pp. 109- 120 ,(2010) , 10.1007/978-3-642-16181-0_10
Michael Fellows, Michael Hallett, Ulrike Stege, On the Multiple Gene Duplication Problem international symposium on algorithms and computation. pp. 347- 356 ,(1998) , 10.1007/3-540-49381-6_37
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, André Wehe, Heuristics for the gene-duplication problem: a Θ(n) speed-up for the local search research in computational molecular biology. pp. 238- 252 ,(2007) , 10.1007/978-3-540-71681-5_17
Cedric Chauve, Nadia El-Mabrouk, New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees Lecture Notes in Computer Science. pp. 46- 58 ,(2009) , 10.1007/978-3-642-02008-7_4
Alix Boc, Vladimir Makarenkov, New Efficient Algorithm for Detection of Horizontal Gene Transfer Events workshop on algorithms in bioinformatics. pp. 190- 201 ,(2003) , 10.1007/978-3-540-39763-2_15
Tobias Hill, Karl JV Nordström, Mikael Thollesson, Tommy M Säfström, Andreas KE Vernersson, Robert Fredriksson, Helgi B Schiöth, SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees BMC Evolutionary Biology. ,vol. 10, pp. 42- 42 ,(2010) , 10.1186/1471-2148-10-42
Ran Libeskind-Hadas, Michael A. Charleston, On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem Journal of Computational Biology. ,vol. 16, pp. 105- 117 ,(2009) , 10.1089/CMB.2008.0084
Magnus Bordewich, Charles Semple, On the computational complexity of the rooted subtree prune and regraft distance. Annals of Combinatorics. ,vol. 8, pp. 409- 423 ,(2005) , 10.1007/S00026-004-0229-Z