Entropy – Uses an EM algorithm for Haplotype Frequency Estimation

Entropy

:: DESCRIPTION

Entropy is a PERL program that uses an EM algorithm for haplotype frequency estimation. It reads standard linkage format files.

::DEVELOPER

Institute for Clinical Molecular Biology

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows
  • Perl

:: DOWNLOAD

 Entropy

:: MORE INFORMATION

Citation

Hampe J, Schreiber S, Krawczak M (2003).
Entropy-based SNP selection for genetic association studies.
Hum Genet 114(1): 36-43

HapSim 0.31 – Haplotype Data Simulation

HapSim 0.31

:: DESCRIPTION

HapSim is a package for haplotype data simulation. Haplotypes are generated such that their allele frequencies and linkage disequilibrium coefficients match those estimated from an input data set.

::DEVELOPER

Giovanni Montana

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • R package

:: DOWNLOAD

 HapSim

:: MORE INFORMATION

Citation

Bioinformatics. 2005 Dec 1;21(23):4309-11. Epub 2005 Sep 27.
HapSim: a simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients.
Montana G.

eHAP 2.0 – Analyze Multilocus data as Haplotypes

eHAP 2.0

:: DESCRIPTION

The eHap software is designed to analyze multilocus data as haplotypes, and to determine whether there is an association between haplotypes and phenotypes. This version of eHap embodies a broad (and ever broadening) set of tools for haplotype-based inference for association (and linkage) studies using population- and family-based samples.

::DEVELOPER

The Devlin lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 eHap

:: MORE INFORMATION

 

CLUMPHAP 1.1 – Haplotype-based Association Analysis

CLUMPHAP 1.1

:: DESCRIPTION

CLUMPHAP implements a novel method for association testing based on clustering similar haplotypes (Knight et al. Submitted). This represents an extension of the basic methodology used in CLUMP, a program designed for the analysis of multi-allelic markers (Sham and Curtis 1995). CLUMPHAP calculates chi-squared statistics for binary partitions of haplotypes, where the number of partitions is reduced by allowing only those that are supported by a hierarchical cluster analysis of the haplotypes. CLUMPHAP obtains the empirical significance level of the largest chi-square statistic by a permutation procedure in which multiple permuted datasets (where the case-control labels have been randomly re-assigned) are subjected to exactly the same procedure of haplotype partitioning and calculation of largest chi-square statistic. Incidentally, this permutation procedure accounts for not only the inflation of the test statistic due to the maximization over the multiple ways of partitioning the haplotypes, but also for the uncertainty in haplotype phase of the individual subjects (Curtis and Sham 2006). The results are easy to interpret, a significant result suggests that a disease causing variant is present on haplotypes in the group which has an increased overall frequency in cases. CLUMPHAP reports the cluster pattern that resulted in the highest chi-squared along with the corresponding statistic and the empirical p-value.

::DEVELOPER

Dave Curtis

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

CLUMPHAP

:: MORE INFORMATION

Citation:

Knight J, Curtis D, Sham PC (submitted)
CLUMPHAP: A simple tool for performing haplotype-based association analysis.
Genet Epidemiol. 2008 Sep;32(6):539-45.

Ehapp – Estimate Haplotype Frequency from Pooled Sequencing data

Ehapp

:: DESCRIPTION

Taking advantage of prior haplotype database, Ehapp implements lsqnonneg and GPSR algrithm to estimate the frequencies of haplotypes from pooled sequencing data.

::DEVELOPER

Bioinfomatics Lab of SouthEast Universtity

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 Ehapp

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 9. pii: btu670.
Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing.
Cao CC1, Sun X

HaploSearch – Haplotype-sequence Two-way Transformation

HaploSearch

:: DESCRIPTION

HaploSearch is a simple tool for transforming DNA sequences into haplotype data and vice versa, speeding up the manipulation of large datasets.

::DEVELOPER

Sergio Delgado Quintero

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

HaploSearch

:: MORE INFORMATION

Citation

Mitochondrion. 2011 Mar;11(2):366-7. doi: 10.1016/j.mito.2010.11.001. Epub 2010 Nov 6.
HaploSearch: a tool for haplotype-sequence two-way transformation.
Fregel R1, Delgado S.

harp 20140925 – Haplotype Analysis of Reads in Pools

harp 20140925

:: DESCRIPTION

harp : Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data. harp implements an EM algorithm to calculate the frequencies of known haplotypes from pooled sequence data.

::DEVELOPER

Novembre Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 harp

 :: MORE INFORMATION

Citation

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data
Darren Kessner; Tom Turner; John Novembre
Mol Biol Evol (2013) 30 (5): 1145-1158. doi: 10.1093/molbev/mst016

hapQTL 0.99 – Haplotype Quantitative Loci

hapQTL 0.99

:: DESCRIPTION

hapQTL performs association testing between local haplotypes and phenotypes at each core marker.

::DEVELOPER

Yongtao Guan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac

:: DOWNLOAD

 hapQTL

:: MORE INFORMATION

Citation

Genetics. 2014 Jul;197(3):823-38. doi: 10.1534/genetics.114.164814. Epub 2014 May 8.
Detecting local haplotype sharing and haplotype association.
Xu H, Guan Y

gTDT 0.01 – A group-wise TDT for Haplotype-based Association Testing of Rare Variants with complex Disease

gTDT 0.01

:: DESCRIPTION

gTDT implemented gene-based or group-wise TDT for rare variant aggregation analysis. Currently gTDT implemented haplotype-based tests for 6 models, M1-M6. It takes as input a ped file and a dat file that specify the relationships, and a VCF file that stores genotype data.

::DEVELOPER

gTDT team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 gTDT 

:: MORE INFORMATION

Citation

A haplotype-based framework for group-wise transmission/disequilibrium tests for rare variant association analysis.
Chen R, Wei Q, Zhan X, Zhong X, Sutcliffe J, Cox N, Cook EH, Li C, Chen W, Li B.
Bioinformatics. 2015 Jan 6. pii: btu860.

PEDIBD – Pedigree IBD & Haplotype Inference

PEDIBD

:: DESCRIPTION

PEDIBD infers pairwise Infer identical-by-descent (IBD) and skips haplotype and inheritance construction

::DEVELOPER

Xin Li 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MatLab

:: DOWNLOAD

  PEDIBD

:: MORE INFORMATION

Citation

J Comput Biol. 2011 Nov;18(11):1411-21. doi: 10.1089/cmb.2011.0167. Epub 2011 Sep 16.
Haplotype reconstruction in large pedigrees with untyped individuals through IBD inference.
Li X1, Li J.