iXora: Haplotype Inferencing and Trait Association

iXora is a framework for inferring haplotypes from genomic marker data, on a population arising from a cross between two heterozygous parents; and subsequently utilizing the haplotypes to map genomic regions associated with observed phenotypes. Each allele in the progeny is assigned not just to a parent, but more precisely to a haplotype of the parent. This finer resolution in inheritance from the parents allows for more accurate association studies, hypothesis checking, as well as randomization tests.

At the core of iXora is a novel exact haplotype inference algorithm that scales to large datasets. The algorithm provides a framework for examining the space of all equally-likely "best" solutions, and computes measures of preciseness regarding the stability of the solutions.

The iXora framework also includes built-in statistical tests, randomization procedures, and visualization tools. The framework is especially well suited to plant breeding, where mapping populations of individuals of inbred (or non-inbred) parents are utilized; iXora has been successfully applied to localize the pod color phenotype in T. cacao.

iXora is available for non-commercial use from http://researcher.ibm.com/project/3430