The program ISHAPE allows a rapid and accurate inference of haplotypes from population genotype data. It first uses a rapid boostrap step of iterative EM (IEM) haplotyping in randomly chosen samples of the population in order to delimit the space of haplotype pairs that will be assigned to the population. It then uses a Phase 2.1-like algorithm to precisely infer haplotypes in the population, within the limits of the previously defined haplotype space. The first bootstrap-IEM step is very rapid, while the second Phase 2.1-like step is also quite rapid since it works on a small working space of haplotypes.

Overall, ISHAPE is much faster than Phase 2.1 and slightly more precise for haplotyping SNPs exhibiting a rather high LD in the population, such as SNPs within a given gene. It will work better for Asian or Caucasian populations which exhibit a lower diversity.

For any use of ISHAPE or publication one must cite :

Delaneau O, Coulonges C, Boelle PY, Nelson G, Spadoni JL, Zagury JF. ISHAPE: new rapid and accurate software for haplotyping. BMC Bioinformatics. 2007;8:205


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