HLA/Estihaplo

EstiHaplo is a software for haplotype estimation frequency estimation developed by P.A. Gourraud and colleagues in . It is based on maximum likelyhood framework using the expectation-maximization (EM) approach. Both commercial and non commercial similar software are available, but this Estihaplo has been specifically developed for large datatsets in the light of handling specifically complex data such as KIR genotype data, HLA typing data, Microsatellites and SNP.

The major functionalities of EstiHaplo are :

• The capacity of inputting phased data.
• An optimisation of the haplotype identification procedure.
• The capacities of handling large dataset of multiallelic loci. (successfully tested for more than 1 million individuals)
• The extensions of the initial mathematical method for the presence of ambiguity in genetic typing including when genes are present in various copies (copy number variant CNV).
• The extensions of the initial mathematical method of the possibility to quantitavely constrain the likelihood model setting the initial values of possible haplotypes at the first step of the EM algorithm.

We here release the most up-to date version, provide as is, it should be considered as a beta release.