A novel exploratory method for visual recombination detection

Genome Biology

Volumn 4, Issue 5, 2003, Pages

  Strimmer, Korbinian ^a   Forslund, Kristoffer ^b   Holland, Barbara ^c   Moulton, Vincent ^b  

^a UNIVERSITY OF MUNICH   (Germany)

^b UPPSALA UNIVERSITY   (Sweden)

^c Allan Wilson Centre for Molecular Ecology & Evolution   (New Zealand)

Author keywords

Influenza; Recombination Breakpoint; Recombination Signal; Slide Window Approach; Window Size

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; COMPUTER SIMULATION; GENETIC DATABASE; GENETIC RECOMBINATION; GENETICS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS 1; METHODOLOGY; ORTHOMYXOVIRUS; PHYLOGENY; SEQUENCE ALIGNMENT;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DATABASES, GENETIC; HIV-1; HUMANS; MODELS, GENETIC; ORTHOMYXOVIRIDAE; PHYLOGENY; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT;

EID: 0038342997     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2003-4-5-r33     Document Type: Article

References (30)

1. Schierup MH, Hein J: Recombination and the molecular clock. Mol Biol Evol. 2000, 17: 1578-1579. DOI: 10.1093/oxfordjournals.molbev.a026256
2. Schierup MH, Hein J: Consequences of recombination on traditional phylogenetic analysis. Genetics. 2000, 156: 879-891.
3. Posada D, Crandall KA: Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol. 2001, 16: 37-45. 10.1016/S0169-5347(00)02026-7. DOI: 10.1016/S0169-5347(00)02026-7
4. Posada D, Crandall KA: The effect of recombination on the accuracy of phylogeny reconstruction. J Mol Evol. 2002, 54: 396-402. DOI: 10.1007/s00239-001-0034-9
5. Wiuf C, Christensen T, Hein J: A simulation study of the reliability of recombination detection methods. Mol Biol Evol. 2001, 18: 1929-1939. DOI: 10.1093/oxfordjournals.molbev.a003733
6. Posada D, Crandall KA: Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci USA. 2001, 98: 13757-13762. 10.1073/pnas.241370698. DOI: 10.1073/pnas.241370698
7. Posada D: Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol. 2002, 19: 708-717. DOI: 10.1093/oxfordjournals.molbev.a004129
8. Brown CJ, Garner EC, Dunker AK, Joyce P: The power to detect recombination using the coalescent. Mol Biol Evol. 2001, 18: 1421-1424. DOI: 10.1093/oxfordjournals.molbev.a003927
9. Salminen M, Carr JK, Burke DS, McCutchan FE: Identification of recombination breakpoints in HIV-1 by bootscanning. AIDS Res Hum Retroviruses. 1995, 11: 1423-1425. DOI: 10.1089/aid.1995.11.1423
10. Sawyer S: Statistical tests for detecting gene conversion. Mol Biol Evol. 1989, 6: 526-536.
11. Worobey M: A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria. Mol Biol Evol. 2001, 18: 1425-1434. DOI: 10.1093/oxfordjournals.molbev.a003928
12. McGuire G, Wright F, Prentice MJ: A Bayesian model for detecting past recombination events in DNA multiple alignments. J Comput Biol. 2000, 7: 159-170. 10.1089/10665270050081432. DOI: 10.1089/10665270050081432
13. Strimmer K, von Haeseler A: Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci USA. 1997, 94: 6815-6819. 10.1073/pnas.94.13.6815. DOI: 10.1073/pnas.94.13.6815
14. Nieselt-Struwe K, von Haeseler A: Quartet-mapping, a generalization of the likelihood-mapping procedure. Mol Biol Evol. 2001, 18: 1204-1219. DOI: 10.1093/oxfordjournals.molbev.a003907
15. Holland B, Huber K, Dress A, Moulton V: Delta-plots: A tool for the analysis of phylogenetic distance data. Mol Biol Evol. 2002, 19: 2051-2059. DOI: 10.1093/oxfordjournals.molbev.a004030
16. Rambaut A, Grassly NC: Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 1997, 13: 235-238.
17. Gao F, Robertson DL, Carruthers CD, Morrison SG, Jian B, Chen Y, Barre-Sinoussi F, Girard M, Srinivasan A, Abimiku AG, et al: A comprehensive panel of near-full-length clones and reference sequences for non-subtype B isolates of human immunodeficiency virus type 1. J Virol. 1998, 72: 5680-5698.
18. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, Ingersoll R, Sheppard HW, Ray SC: Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol. 1999, 73: 152-160.
19. Gibbs MJ, Armstrong JS, Gibbs AJ: Recombination in the hemagglutinin gene of the 1918 "Spanish flu". Science. 2001, 293: 1842-1845. 10.1126/science.1061662. DOI: 10.1126/science.1061662
20. Worobey M, Rambaut A, Pybus OG, Robertson DL: Questioning the evidence for genetic recombination in the 1918 "Spanish flu" virus. Science. 2002, 296: 211-10.1126/science.296.5566.211a. DOI: 10.1126/science.296.5566.211a
21. Grassly NC, Holmes EC: A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol Biol Evol. 1997, 14: 239-247. DOI: 10.1093/oxfordjournals.molbev.a025760
22. Hein J: Reconstructing evolution of sequences subject to recombination used parsimony. Math Biosci. 1990, 98: 185-200. 10.1016/0025-5564(90)90123-G. DOI: 10.1016/0025-5564(90)90123-G
23. Schmidt HA, Strimmer K, Vingron M, von Haeseler A: TREE-PUZZLE: maximum-likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002, 18: 502-504. 10.1093/bioinformatics/18.3.502. DOI: 10.1093/bioinformatics/18.3.502
24. RecPars - Parsimony analysis of DNA sequences. [http://www.daimi.au.dk/~compbio/recpars/recpars.html]
25. Tukey JW: Exploratory Data Analysis. Reading, MA: Addison-Wesley. 1977
26. Eigen M, Winkler-Oswatitsch R, Dress A: Statistical geometry in sequence space: a method of quantitative comparative sequence analysis. Proc Natl Acad Sci USA. 1988, 85: 5913-5917. DOI: 10.1073/pnas.85.16.5913
27. Wegman EJ: Data mining and visualization: some strategies. Bull Int Statist Inst. 1999, 52: 223-226.
28. Ball P: Picture this. Nature. 2002, 418: 11-13. 10.1038/418011a. DOI: 10.1038/418011a
29. Jobb G: Eine Maximum-Likelihood Methode zum Aufspüren phylogenetischer Inhomogenitäten in molekularen Datensätzen. Master's thesis. Munich: University of Munich. 1999
30. VisRD: Visual Recombination Detection. [http://www.lcb.uu.se/~vmoulton/software]