Algorithms: Simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem

BMC Bioinformatics

Volumn 13, Issue , 2012, Pages

  Górecki, Pawel ^a   Eulenstein, Oliver ^b  

^a UNIVERSITY OF WARSAW   (Poland)

^b Iowa State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; ERROR CORRECTION; ERRORS; EVOLUTIONARY ALGORITHMS; FORESTRY; TREES (MATHEMATICS);

CORRECTION APPROACHES; ERROR-CORRECTING; EVOLUTIONARY EVENTS; EVOLUTIONARY METHOD; GENE DUPLICATIONS; PHYLOGENETIC STUDIES; RECONCILIATION PROCESS; TOPOLOGICAL ERRORS;

GENES;

EXPERIMENTAL MODEL; GENE DUPLICATION; ROOTING; SPECIES; ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; GENETICS; GENOMICS; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; YEAST;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DUPLICATION; GENOMICS; MODELS, GENETIC; PHYLOGENY; SOFTWARE; YEASTS;

EID: 84877152040     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S10-S14     Document Type: Article

References (25)

1. Graur D, Li WH: Fundamentals of Molecular Evolution. 2 edition. Sinauer Associates; 2000 [http://www.amazon.com/exec/obidos/redirect?tag=citeulike07-20\&path=ASIN/0878932666]
2. Page RDM: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology 1994, 43:58-77
3. Bonizzoni P, Della Vedova G, Dondi R: Reconciling a gene tree to a species tree under the duplication cost model. Theoretical Computer Science 2005, 347(1-2):36-53
4. Eulenstein O, Mirkin B, Vingron M: Duplication-Based Measures of Difference Between Gene and Species Trees. J Comput Biol 1998, 5:135-148
5. Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G: Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences. Systematic Zoology 1979, 28(2):132-163
6. Mirkin B, Muchnik IB, Smith TF: A Biologically Consistent Model for Comparing Molecular Phylogenies. J Comput Biol 1995, 2(4):493-507
7. Sanderson M, McMahon M: Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evolutionary Biology 2007, 7(Suppl 1)[http://dx.doi.org/10.1186/1471-2148-7-S1-S3]
8. Bansal MS, Eulenstein O: The multiple gene duplication problem revisited. Bioinformatics 2008, 24(13):i132-8
9. Fellows MR, Hallett MT, Stege U: On the Multiple Gene Duplication Problem. In ISAAC, Volume 1533 of LNCS Chwa KY, Ibarra OH, Springer 1998, 347-356
10. Guigó R, Muchnik IB, Smith TF: Reconstruction of ancient molecular phylogeny. Molecular Phylogenetics and Evolution 1996, 6(2):189-213
11. Behzadi B, Vingron M: Reconstructing Domain Compositions of Ancestral Multi-domain Proteins. In Comparative Genomics, Volume 4205 of LNCS. Springer;Bourque G, El-Mabrouk N 2006:1-10
12. Bansal MS, Burleigh GJ, Eulenstein O, Wehe A: Heuristics for the Gene-Duplication Problem: A Θ(n) Speed-Up for the Local Search. RECOMB, Volume 4453 of LNCS Springer; 2007, 238-252
13. Ma B, Li M, Zhang L: From Gene Trees to Species Trees. SIAM Journal on Computing 2000, 30(3):729-752
14. Page RDM: GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 1998, 14(9):819-820
15. Hahn MW: Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome biology 2007, 8(7):R141[http://dx.doi.org/10.1186/gb-2007-8-7-r141]
16. Chen K, Durand D, Farach-Colton M: NOTUNG: a program for dating gene duplications and optimizing gene family trees. J Comput Biol 2000, 7(3-4):429-447
17. Durand D, Halldorsson BV, Vernot B: A Hybrid Micro-Macroevolutionary Approach to Gene Tree Reconstruction. J Comput Biol 2006, 13(2):320-335 [http://dx.doi.org/10.1089/cmb.2006.13.320]
18. Górecki P, Tiuryn J: Inferring phylogeny from whole genomes. Bioinformatics 2007, 23(2):e116-22
19. Wehe A, Bansal MS, Burleigh GJ, Eulenstein O: Dup-Tree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 2008, 24(13):1540-1541
20. Eulenstein O, Huzurbazar S, Liberles D: Reconciling phylogenetic trees. Evolution After Gene Duplication Dittmar, Liberles, Wiley; 2010
21. Bender MA, Farach-Colton M: In The LCA Problem Revisited LATIN, Volume 1776 of LNCS. Springer;Gonnet GH, Panario D, Viola A 2000:88-94
22. Górecki P, Eulenstein O: A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees. In Bioinformatics Research and Applications, Volume 6674 of Lecture Notes in Computer Science. Springer Berlin/Heidelberg;Chen J, Wang J, Zelikovsky A 2011:148-159
23. Górecki P, Tiuryn J: URec: a system for unrooted reconciliation. Bioinformatics 2007, 23(4):511-512
24. Sherman DJ, Martin T, Nikolski M, Cayla C, Souciet JL, Durrens P: Gènolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. Nucleic Acids Research 2009, 37(suppl 1):D550-D554[http://nar.oxfordjournals.org/content/37/suppl_1/D550.abstract]
25. Notredame C, Higgins DG, Jaap H: T-coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol 2000, 302:205-217 [http://dx.doi.org/10.1006/jmbi.2000.4042]