Inferring horizontal transfers in the presence of rearrangements by the minimum evolution criterion

Bioinformatics

Volumn 24, Issue 6, 2008, Pages 826-832

  Birin, Hadas ^a   Gal Or, Zohar ^a   Elias, Isaac ^b   Tuller, Tamir ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CONTROLLED STUDY; CYANOBACTERIUM; EVOLUTION; GENE DELETION; GENE DUPLICATION; GENE INSERTION; GENE REARRANGEMENT; GENETIC RECOMBINATION; HORIZONTAL GENE TRANSFER; MOLECULAR PHYLOGENY; NONHUMAN; PLANT; PLASTID; POINT MUTATION; PRIORITY JOURNAL; PROTEOBACTERIA; SEQUENCE ALIGNMENT; SIMULATION;

EID: 40749139524     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn024     Document Type: Article

References (33)

1. Addario-Berry,L. et al. (2003) Towards identifying lateral gene transfer events. In PSB03. pp. 279-290.
2. Arvestad,L. et al. (2006) Beep software package.
3. Bergthorsson,U. et al. (2003) Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature, 424, 197-201.
4. Boc,A and Makarenkov,V. (2003) New efficient algorithm for detection of horizontal gene transfer events. In WABI. pp. 190-201.
5. Burkhardt,S. and Kärkkäinen,J. (2003) Fast lightweight suffix array construction and checking. In Baeza-Yates,R., Chávez,E. and Crochemore,M. (eds.) Proceedings of 14th Symposium on Combinatorial Pattern Matching (CPM'03). Springer-Verlag, Berlin Heidelberg, pp. 55-69.
6. Delwiche,C. and Palmer,J. (1996) Rampant horizontal transfer and duplicaion of rubisco genes in eubacteria and plastids. Mol. Biol. Evol., 13, 873-882.
7. Desper,R. and Gascuel,O. (2002) Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comp. Biol., 9, 687-705.
8. Doolittle,W.F. et al. (2003) How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Phil. Trans. R. Soc. Lond. B. Biol. Sci., 358, 39-57.
9. Elias,I. (2003) Sealing the intractability of multiple alignment. In ISAAC. pp. 352-363.
10. Felsenstein,J. (1978) Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool., 27, 27-33.
11. Felsenstein,J. (1993) Phylip (phylogeny inference package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
12. Gascuel,O. (1997) Concerning the NJ algorithm and its unweighted version UNJ. In Mirkin,B et al. (ed.) Mathematical hierarchies and Biology. DIMACS Series in Discrete Mathematics and Theoretical Computer Science 37, Amerrican Mathematical Society, Providence, R.I.
13. Gompels,U.A. et al. (1995) The DNA sequence of human herpesvirus-6: Structure, coding content, and genome evolution. Virology, 209, 29-51.
14. Hein,J. (1993) A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol., 36, 396-405.
15. Huson,D.H. and Bryant,D. (2006) Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol, 23, 254-267.
16. Guohua,J. et al. (2006) Maximum likelihood of phylogenetic networks. Bioinformatics, 22, 2604-2611.
17. Guohua,J. et al. (2007) Inferring phylogenetic networks by the maximum parsimony criterion: A case study. Mol. Biol. Evol., 24 324-337.
18. Judd,W.S. and Olmstead,R.G. (2004) A survey of tricolpate (eudicot) phylogenetic relationships. Am. J. Bot., 91, 1627-1644.
19. Kalinina,O. et al. (2004) Full-length open reading frame of a recombinant Hepatitis C virus strain from St Petersburg: Proposed mechanism for its formation. J. Gen. Virol., 85, 1853-1857.
20. Kidd,K.K. and Sgaramella-Zonta,L.A. (1971) Phylogenetic analysis: concepts and methods. Am. J. Hum. Genet., 23, 235-252.
21. Koonin,E.V. et al. (2006) The ancient virus world and evolution of cells, Biol. Direct., 1.
22. Kuiken,C. et al. (2005) The los alamos HCV sequence database. Bioinformatics, 21, 379-84.
23. Michelangeli,F.A. et al. (2003) Phylogonetic relationships among Poaceae and related families as inferred from morphology, inversions in the plastid genome, and sequence data from mitochondrial and plastid genomes. Am. J. Bot., 90, 93-106.
24. Rzhetsky,A. and Nei,M. (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10, 1073-1095.
25. Saitou,N. and Nei,M. (1997) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-25.
26. Sinkovics,J. et al. (1998) The origin and evolution of viruses (a review). Acta Microbiol Immunol Hung., 45, 349-390.
27. Smith,D.B. et al. (1997) The origin of hepatitis C virus genotypes. J. Gen. Virol., 78, 321-328.
28. Stoye,J. et al. (1998) Rose: Generating sequence families. Bioinformatics, 14, 157-163.
29. Strimmer,K. and Moulton,V. (2000) Likelihood analysis of phylogenetic networks using directed graphical models. Mol. Biol. Evol., 17 875-881.
30. Susko,E. et al. (2004) On inconsistency of the neighbor-joining, least squares, and minimum evolution estimation when substitution processes are incorrectly modeled. Mol. Biol. Evol., 21, 1629-1642.
31. Ulitsky,I. et al. (2006) The average common substring approach to phylogenomic reconstruction. J. Comp. Biol., 13, 336-350.
32. Worobey,M. and Holmes,E.C. (1999) Evolutionary aspects of recombination in RNA viruses. J. Gen. Virol., 80, 2535-2543.
33. Xu,L. et al. (2006) Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms. Mol. Biol. Evol., 23, 1107-1108.