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This article is part of the supplement: Proceedings of the 12th European workshop on QTL mapping and marker assisted selection

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Haplotyping via minimum recombinant paradigm

Jules Hernández-Sánchez* and Sara Knott

Author Affiliations

Institute of Evolutionary Biology, University of Edinburgh, King's Buildings (Ashworth Laboratories), West Main Roads, EH9 3JT, Edinburgh, UK

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BMC Proceedings 2009, 3(Suppl 1):S7  doi:10.1186/1753-6561-3-S1-S7

Published: 23 February 2009



Haplotypes can increase the power of gene detection over genotypes and are essential to estimate linkage disequilibrium.


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.


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.


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.