DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony

Bioinformatics

Volumn 24, Issue 13, 2008, Pages 1540-1541

  Wehe, André ^a   Bansal, Mukul S ^a   Burleigh, J Gordon ^b   Eulenstein, Oliver ^a  

^a Iowa State University   (United States)

^b NESCent   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; GENE DUPLICATION; GENE LOSS; GENE NUMBER; GENE TREE PARSIMONY; GENETIC ALGORITHM; GENETIC DATABASE; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; PARSIMONY ANALYSIS; PHYLOGENETIC TREE ROOT; PHYLOGENY; PRIORITY JOURNAL;

EID: 46249126320     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn230     Document Type: Article

References (15)

1. 2/logn) speed-up of TBR heuristics for the gene-duplication problem. In Giancario,R. and Hannenballi,S. (eds) Proceedings of the 7th International Workshop on Algorithms in Bioinformatics (WABI'07). Vol. 4645 in Lecture Notes in Computer Science, Springer, Philadelphia, PA, USA, pp. 124-135.
2. Bansal,M.S. et al. (2007) Heuristics for the gene-duplication problem: A θ(n) speedup for the local search. In Speed,T.P. and Huang,H. (eds) Proceedings of the 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB'07) Vol. 4453 in Lecture Notes in Computer Science, Springer, Oakland, CA, USA, pp. 238-252.
3. Ma,B. et al.(1998) On reconstructing species trees from gene trees in term of duplications and losses. In Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology. ACM, New York, NY, USA, pp. 182-191.
4. Maddison,W.P. (1997) Gene trees in species trees. Syst. Biol., 46, 523-536.
5. Page,R.D.M. (1995) Program COMPONENT. Available at http://taxonomy.zoology.gla.ac.uk/rod/cpw.html. (last accessed date June 3, 2008).
6. Page,R.D.M. (1998) GeneTree: Comparing gene and species phylogenies using reconciled trees. Bioinformatics, 14, 819-820.
7. Page,R.D.M. (2000) Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny. Mol. Phylogenet. Evol., 14, 89-106.
8. Page,R.D.M. and Charleston,M.A. (1997) Reconciled trees and incongruent gene and species trees. In Mirkin,B. et al. (eds) Mathematical Hierarchies in Biology. Vol. 37. American Mathematical Society, Providence, Rhode Island, USA, pp. 57-70.
9. Page,R.D.M. and Cotton,J. (2002) Vertebrate phylogenomics: Reconciled trees and gene duplications. In Altman,R.B. et al. (eds) Proceedings of the 7th Pacific Symposium on Biocomputing (PSB'02). Lihue, Hawaii, USA, pp. 536-547.
10. Sanderson,M.J. and McMahon,M.M. (2007) Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evol. Biol., 7 (Suppl. 1), S3.
11. Semple,C. and Steel,M. (2003) Phylogenetics. Oxford University Press, New York, NY, USA.
12. Simmons,M.P. et al. (2000) Phylogenctic reconstruction using duplicate genes. Mol. Biol. Evol., 17, 469-473.
13. Slowinski,J. and Page,R.D.M. (1999) How should species phylogenics be inferred from sequence data? Syst. Biol., 105, 147-158.
14. Slowinski,J.B. et al. (1997) Inferring species trees from gene trees: A phylogenetic, analysis of the elapidae (serpentes) based on the amino acid sequences of venom proteins. Mol. Phylogenet. Evol., 8, 349-362.
15. Zhang,L. (1997) On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J. Comput. Biol., 4, 177-187.