:: DESCRIPTION
SharedHap computes and visualize Haplotype-Sharing Patterns among subjects of interests in a pedigree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Hum Hered. 2014;78(1):1-8. doi: 10.1159/000358171.
Visualization of haplotype sharing patterns in pedigree samples.
Kim S1, Saad M, Tsuang DW, Wijsman EM.
:: DESCRIPTION
HaploPOP is a software to build informative haplotypes for population genetic structure inference.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
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)
:: DESCRIPTION
Fitchi is a python script that produces haplotype genealogy graphs from alignment files in Nexus format, along with summary statistics.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Fitchi: Haplotype genealogy graphs based on the Fitch algorithm.
Matschiner M.
Bioinformatics. 2015 Dec 9. pii: btv717.
:: DESCRIPTION
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.
::DEVELOPER
Rosenberg lab at Stanford University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Innan H, Zhang K, Marjoram P, Tavaré S, Rosenberg NA.
Statistical tests of the coalescent model based on the haplotype frequency distribution and the number of segregating sites
Genetics 169: 1763-1777 (2005)
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
::REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
HapCol: Accurate and Memory-efficient Haplotype Assembly from Long Reads.
Pirola Y, Zaccaria S, Dondi R, Klau GW, Pisanti N, Bonizzoni P.
Bioinformatics. 2015 Aug 26. pii: btv495
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2014 May 30;15(1):164. [Epub ahead of print]
WinHAP2: an extremely fast haplotype phasing program for long genotype sequences.
Pan W, Zhao Y, Xu Y, Zhou F.
PLoS One. 2012;7(8):e43163. doi: 10.1371/journal.pone.0043163. Epub 2012 Aug 14.
WinHAP: an efficient haplotype phasing algorithm based on scalable sliding windows.
Xu Y1, Cheng W, Nie P, Zhou F.
:: DESCRIPTION
SNPHAP is a program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects
::DEVELOPER
David Clayton (david.clayton@cimr.cam.ac.uk)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
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.
::DEVELOPER
Department of Bioinformatics, University of Tartu
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
PLoS One. 2015 Apr 8;10(4):e0122713. doi: 10.1371/journal.pone.0122713. eCollection 2015.
Haplotype phasing and inheritance of copy number variants in nuclear families.
Palta P, Kaplinski L, Nagirnaja L, Veidenberg A, Möls M, Nelis M, Esko T, Metspalu A, Laan M, Remm M
:: DESCRIPTION
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
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Carr IM, Diggle DP, Touqan N, Anwar R, Sheridan EG, Bonthron DT, Johnson CA, Ali M, Markham AF.
Identification of autosomal recessive disease loci using out-bred nuclear families.
Hum Mutat. 2012 Feb;33(2):338-42.
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Sep 15;29(18):2245-52. doi: 10.1093/bioinformatics/btt386.
Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.
Yang WY, Hormozdiari F, Wang Z, He D, Pasaniuc B, Eskin E.
