Haplotype

HapEdit is an instrument that's been specially built in order to help the user assess the accuracy of haplotype assembly. This is done using the next-generation sequencing technologies. HapEdit is a tool that was created with the help of the Java programming language and can run on multiple...

GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.

HaploView is a Java based tool for use by biologists in the study of genetic haplotype data. It provides a quick, easy interface to many common tasks involved in such analyses.


Platforms: Windows, Mac, Linux

The annotation files for Illumina SNP genotyping platforms generated for performing Homozygosity Haplotype analysis


Platforms: Windows, Mac, Linux

MAGMA: Multiobjective Analyzer for Genetic Marker AcquisitionA genetic algorithm for generating SNP tiling paths from a large SNP databasebased on the competing objectives of cost (number of SNPs) and coverage (haplotype blocks):Hubley R., Zitzler


Platforms: Windows, Mac, Linux

Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. Olorin, is a tool which integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based...


Platforms: Mac

HaploPainter - a pedigree and haplotypes drawing tool written in Perl/Tk. The software processes pedigree information in standard linkage formats combining haplotype information outputs from Simwalk, Genehunter, Allegro and Merlin.


Platforms: *nix

UNPHASED is a small, simple, Java based application specially designed to offer users a versatile tool for performing genetic association analysis. This utility implements maximum-likelihood inference on haplotype and genotype effects while allowing for uncertain phase and missing genotypes....


Platforms: Windows

Olorin is an interactive filtering utility built using the Java programming language. The program can be used for next generation sequencing data coming from the study of large complex disease pedigrees. Olorin, is a tool which integrates gene flow output from Merlin and next generation...


Platforms: Windows

Diversity Maps is a data visualization tool for plant geneticists and breeders. It generates publication-quality, vector-based chromosome maps displaying differences in marker states between individuals. Features Displays haplotype similarity by color; Sorts accessions automatically to...


Platforms: *nix