Bioinformatics Vol. 16 no. 2 2000
Pages 130-134
© 2000 Oxford University Press
TOPAL 2.0: improved detection of mosaic sequences within multiple alignments
1 Isaac Newton Institute for Mathematical
Sciences, 20 Clarkson Road, Cambridge CB3 0EH, UK
2 Biomathematics and Statistics Scotland,
Scottish Crop Research Institute, Dundee DD2 5DA, UK
Present address: Department of Applied Statistics, PO Box 240, Harry Pitt Building, University of Reading, Reading RG6 6FN, UK
To whom correspondence should be addressed.
Motivation: The Dss statistic was proposed by (Mol. Biol. Evol., 14, 1125–1131, McGuire et al. (1997)) for scanning data sets for the presence of recombination, an important step in some phylogenetic analyses. The statistic, however, could not distinguish well between among-site rate variation and recombination, and had no statistical test for significant values. This paper addresses these shortfalls.
Results: A modification to the Dss statistic is proposed which accounts for rate variation to a large extent. A statistical test, based on parametric bootstrapping, is also suggested.
Availability: The TOPAL package (version 2) may be accessed from http://www.bioss.sari.ac.uk/~frank/Geneticsand by anonymous ftp from ftp://ftp.bioss.sari.ac.ukin the directory pub/phylogeny/topal.
Contact: frank{at}bioss.sari.ac.uk
Received on June 28, 1999
; revised on August 18, 1999
; accepted on August 23, 1999
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  A. D. Leache Species Tree Discordance Traces to Phylogeographic Clade Boundaries in North American Fence Lizards (Sceloporus) Syst Biol, December 1, 2009; 58(6): 547 - 559. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. D. Leache, M. S. Koo, C. L. Spencer, T. J. Papenfuss, R. N. Fisher, and J. A. McGuire From the Cover: Quantifying ecological, morphological, and genetic variation to delimit species in the coast horned lizard species complex (Phrynosoma) PNAS, July 28, 2009; 106(30): 12418 - 12423. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. Webb, J. M. Hancock, and C. C. Holmes Phylogenetic inference under recombination using Bayesian stochastic topology selection Bioinformatics, January 15, 2009; 25(2): 197 - 203. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. D. Carling and R. T. Brumfield Integrating Phylogenetic and Population Genetic Analyses of Multiple Loci to Test Species Divergence Hypotheses in Passerina Buntings Genetics, January 1, 2008; 178(1): 363 - 377. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. M. Bergholz, C. L. Tarr, L. M. Christensen, D. J. Betting, and T. S. Whittam Recent Gene Conversions between Duplicated Glutamate Decarboxylase Genes (gadA and gadB) in Pathogenic Escherichia coli Mol. Biol. Evol., October 1, 2007; 24(10): 2323 - 2333. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Maydt and T. Lengauer Recco: recombination analysis using cost optimization Bioinformatics, May 1, 2006; 22(9): 1064 - 1071. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. C. Bruen, H. Philippe, and D. Bryant A Simple and Robust Statistical Test for Detecting the Presence of Recombination Genetics, April 1, 2006; 172(4): 2665 - 2681. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 A. N. Lukashev, V. A. Lashkevich, O. E. Ivanova, G. A. Koroleva, A. E. Hinkkanen, and J. Ilonen Recombination in circulating Human enterovirus B: independent evolution of structural and non-structural genome regions J. Gen. Virol., December 1, 2005; 86(12): 3281 - 3290. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. J. B. Krieger and K. G. Ross Molecular Evolutionary Analyses of the Odorant-Binding Protein Gene Gp-9 in Fire Ants and Other Solenopsis Species Mol. Biol. Evol., October 1, 2005; 22(10): 2090 - 2103. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 Q. Lin and Y. Rikihisa Establishment of Cloned Anaplasma phagocytophilum and Analysis of p44 Gene Conversion within an Infected Horse and Infected SCID Mice Infect. Immun., August 1, 2005; 73(8): 5106 - 5114. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Husmeier, F. Wright, and I. Milne Detecting interspecific recombination with a pruned probabilistic divergence measure Bioinformatics, May 1, 2005; 21(9): 1797 - 1806. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. Liu, J. I. B. Bos, M. Armstrong, S. C. Whisson, L. da Cunha, T. Torto-Alalibo, J. Win, A. O. Avrova, F. Wright, P. R. J. Birch, et al. Patterns of Diversifying Selection in the Phytotoxin-like scr74 Gene Family of Phytophthora infestans Mol. Biol. Evol., March 1, 2005; 22(3): 659 - 672. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. P. Martin, C. Williamson, and D. Posada RDP2: recombination detection and analysis from sequence alignments Bioinformatics, January 15, 2005; 21(2): 260 - 262. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. P. Bielawski, K. A. Dunn, G. Sabehi, and O. Beja Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment PNAS, October 12, 2004; 101(41): 14824 - 14829. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. P. Rooney Mechanisms Underlying the Evolution and Maintenance of Functionally Heterogeneous 18S rRNA Genes in Apicomplexans Mol. Biol. Evol., September 1, 2004; 21(9): 1704 - 1711. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. H. Ardell, C. A. Lozupone, and L. F. Landweber Polymorphism, Recombination and Alternative Unscrambling in the DNA Polymerase {alpha} Gene of the Ciliate Stylonychia lemnae (Alveolata; class Spirotrichea) Genetics, December 1, 2003; 165(4): 1761 - 1777. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. Husmeier and G. McGuire Detecting Recombination in 4-Taxa DNA Sequence Alignments with Bayesian Hidden Markov Models and Markov Chain Monte Carlo Mol. Biol. Evol., March 1, 2003; 20(3): 315 - 337. [Abstract] [Full Text] [PDF]
|
|