Haplofinder is a simple python script designed to simplify identification of possible haplotype pairs when presented with an ambiguous sequence trace derived from a diploid organism. The context in which it was developed is the investigation of immune function in cattle, specifically the development of a sequence-based typing system for exon 2 of the BoLA-DRB3 gene.
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Anim Genet. 2008 Oct;39(5):561-3. doi: 10.1111/j.1365-2052.2008.01757.x. Epub 2008 Jul 15.
A rapid and robust sequence-based genotyping method for BoLA-DRB3 alleles in large numbers of heterozygous cattle.
Baxter R, Hastings N, Law A, Glass EJ.