title: Stepwise detection of recombination breakpoints in sequence alignments.
abstract: BACKGROUND
  We propose a stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints.
  
  
  RESULTS
  We illustrate the approach by analyses of a simulated dataset and alignments of real data from HIV-1 and human chromosome 7. The presented simulation results compare the statistical properties of one-step and two-step procedures. More breakpoints are found with a two-step procedure than with a single application of a given method, particularly for higher recombination rates. At higher recombination rates, the additional breakpoints were located at the cost of only a slight increase in the number of falsely declared breakpoints. However, a large proportion of breakpoints still go undetected.
  
  
  BACKGROUND
  A makefile and C source code for phylogenetic profiling and the maximum chi2 method, tested with the gcc compiler on Linux and WindowsXP, are available at http://stat-db.stat.sfu.ca/stepwise/
  
  
  BACKGROUND
  jgraham@stat.sfu.ca.
authors.affiliation: Department of Statistics and Actuarial Science, Simon Fraser University Burnaby, Canada V5A 1S6. jgraham@stat.sfu.ca
authors.forename: Jinko
authors.initials: J
authors.lastname: Graham
authors.forename: Brad
authors.initials: B
authors.lastname: McNeney
authors.forename: Françoise
authors.initials: F
authors.lastname: Seillier-Moiseiwitsch
mesh_terms: D000465:Algorithms; D019457:Chromosome Breakage / Q000235:genetics*; D002897:Chromosomes, Human, Pair 7 / Q000235:genetics; D003198:Computer Simulation; D016679:Genome, Viral; D015497:HIV-1 / Q000235:genetics; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D010363:Pattern Recognition, Automated / Q000379:methods*; D011995:Recombination, Genetic / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*