title: Haplotyping via minimum recombinant paradigm.
abstract: BACKGROUND
  Haplotypes can increase the power of gene detection over genotypes and are essential to estimate linkage disequilibrium.
  
  
  METHODS
  Haplotyping was based on the minimum recombinant paradigm, whereby a phase is obtained only if it uniquely minimises the number of recombinants within a full sib family. Performance of this method was tested across three different data sets, consisting of genotypes and pedigree.
  
  
  RESULTS
  The percentage of phased alleles ranged from ~80% to ~95%, and the percentage of correct phases reached ~99% in all cases. A measure of uncertainty was obtained via simulations. A partial haplotyping algorithm consisting of four deterministic rules was almost as effective as a full one consisting of six deterministic rules, and took up to 5 times less time to compute.
  
  
  CONCLUSIONS
  Haplotyping via the minimum recombinant paradigm is consistently reliable and computationally efficient. A single simulation is enough to produce a population-wide uncertainty estimate associated with a set of all reconstructed haplotypes.
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, King's Buildings (Ashworth Laboratories), West Main Roads, EH9 3JT, Edinburgh, UK. jules.hernandez@ed.ac.uk
authors.forename: Jules
authors.initials: J
authors.lastname: Hernández-Sánchez
authors.forename: Sara
authors.initials: S
authors.lastname: Knott