Duforet-Frebourg N., Gattepaille L.M., Blum M.G.B and Jakobsson M.
Haplopop: a software that improves population assignment by combining markers into haplotypes.
(in prep)
haploconfig is a program that can be used to implement tests of neutrality based on the frequency distribution of haplotypes in a sample of DNA sequences (the “haplotype configuration”) and the number of segregating sites. The neutrality tests can be performed conditional on the standard neutral coalescent model with or without recombination, exponential population growth, or island migration.
HapCol implements a fixed-parameter algorithm for the k-constrained Minimum Error Correction problem (k-cMEC), a variant of the well-known MEC problem where the maximum number of corrections per column is bounded by an integer k. HapCol, while is as accurate as other exact state-of-the-art combinatorial approaches, is significantly faster and more memory-efficient than them. Moreover, HapCol is able to process datasets composed of both long reads (over 100 000bp long) and coverages up to 25x on standard workstations/small servers, whereas the other approaches cannot handle long reads or coverages greater than 20x.
WinHAP is a fast haplotype phasing program for phasing large-scale population genotypes data. WinHAP2.0 is a significantly improved version of the WinHAP program that both process longer sequences with less computer memory usage and increases computing speed.
PiCNV (Phasing and inheritance of Copy Number Variants) enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data.
Phaser is a program for the rapid identification of linkage to recessive disease genes in either consanguineous or out-bred families, by reconstructing the haplotype for each individual’s chromosomes within a pedigree
HARSH (HAplotype inference using Reference and Sequencing tecHnology) is a method to infer the haplotype using haplotype reference panel and high throughput sequencing data. It is based on a novel probabilistic model and Gibbs sampler method.