Multiple consensus trees: A method to separate divergent genes

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  Guénoche, Alain ^a  

^a AIX MARSEILLE UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

C (PROGRAMMING LANGUAGE); ESCHERICHIA COLI; GENES; HORIZONTAL WELLS; TOPOLOGY;

GENETIC PATTERNS; HORIZONTAL GENE TRANSFER; HORIZONTAL TRANSFER; MULTIPLE CONSENSUS; ORTHOLOGOUS SEQUENCES; PHYLOGENETIC TREES; RESEARCH COMMUNITIES; TOPOLOGICAL GROUPS;

TREES (MATHEMATICS);

BIOINFORMATICS; BOOTSTRAPPING; CONSENSUS; HORIZONTAL GENE TRANSFER; HUMAN; PHYLOGENETIC TREE; SIMULATION; SOFTWARE; ALGORITHM; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; ESCHERICHIA COLI; GENE; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY;

ALGORITHMS; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENES; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

MLCS; MLOWN;

EID: 84873420648     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-46     Document Type: Article

References (19)

1. de Vienne DM, Ollier S, Aguileta G: Phylo-MCOA: a fast and efficient method to detect outlier genes an species in Phylogenomics using multiple co-inertia analysis. Mol Biol Evol 2012, 29(6):1587-1598
2. Semple C, Steel M: Phylogenetics. Oxford: Oxford University Press; 2003
3. Felsenstein J: Inferring Phylogenies. Sunderland: Sinauer Associates; 2002
4. Felsenstein J: Confidence-limits on phylogenies-an approach using the bootstrap. Evolution 1985, 39:783-791
5. Bryant D: A Classification of consensus methods for phylogenetics. In BioConsensus, DIMACS. Edited by Janowitz M, Lapointe FJ, McMorris FR, Mirkin B, Roberts FS. Providence: AMS; 2003:163-184
6. Garrey MR, Johnson DS: Computers and Intractability: A Guide to Theory of NP-Completeness. San Francisco: W.H Freeman; 1979
7. Barthelemy JP, Mc Morris, F R: The median procedure for n-trees. J Classif 1986, 3:329-334
8. Maddison DR: The discovery and importance ofmultiple islands of most-parcimonious trees. Syst Zool 1991, 21:1098-1109
9. Stockham C, Wang LS, Warnow T: Statistically based postprocessing of phylogenetic analysis by clustering. Bioinformatics 2002, 18:S285-S293
10. Bonnard C, Berry V, Lartillot N: Multipolar consensus for phylogenetic trees. Syst Biol 2006, 55(5):837-843
11. Koperwas J, Walczak K: Tree edit distance for leaf-labelled trees on free leafset and its comparison with frequent subsplit dissimilaritiy and popular distancemeasure. BMC Bioinformatics 2011, 12:204
12. Robinson DF, Foulds LR: Comparison of phylogenetic trees. Math Biosc 1981, 53:131-147
13. Estabrook GF, McMorris FR, Meacham CA: Comparison of undirected phylogenetic trees based on subtrees of 4 evolutionary units. Syst Zool 1985, 34:193-200
14. Kimura M: A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. JMol Evol 1980, 16:111-120
15. Brown JR, Douady CJ, Italia MJ, Marshall WE, Stanhope MJ: Universal trees based on large combined protein sequence data sets. Nat Genet 2001, 28:281-285
16. Darlu P, Guenoche A: The TreeOfTrees method to evaluate the congruence between gene trees. J. of Classification 2011, 28(3):390-403
17. Schubert S, Darlu P, Clermont O, et al.: Role of intraspecies recombination in the spead of pathogenicity islands within the Escherichia coli species. PLoSpathogens 2009, 5(1):e1000257
18. Guindon S, Gascuel O: A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003, 52:696-704
19. Lapointe JF, Cucumel G: The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Syst Biol 1997, 462:306-312