A Compilation of Some Available Software for Linkage Disequilibrium Analysis

Available on/from this site
  • MIDAS - interallelic linkage disequilibrium analysis for multiallelic and biallelic markers with interactive graphical interface.
  • CubeX - online web tool for calculation of pairwise linkage disequilibrium using exact solution.

A range of LD software from different authors (in alphabetical order)
  • 2LD: “Two-locus LD calculator for multiallelic markers including SNPs. It computes a number linkage disequilibrium statistics (including the variance of D’ thus providing D’ estimates and standard error) and association tests. It conducts haplotype frequency estimation, including X chromosome data, and uses a heuristic algorithm to handle multiple genetic markers and missing data.” - http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software.htm
  • ALLASS: “Estimates composite linkage disequilibrium for multilocus data using the Malécot isolation by distance equation” - http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ALLASS
  • ARLEQUIN: “Population genetic analysis package that includes haplotype estimation by the EM algorithm and LD analysis for locus pairs; significance tested by permutation method" - http://anthro.unige.ch/arlequin/
  • CubeX: "online web tool for calculation of pairwise linkage disequilibrium using exact solution" - http://www.oege.org/software/cubex/
  • DISEQ : “Multilocus disequilibrium estimation program” - http://linkage.rockefeller.edu/soft/diseq.html
  • DnaSP: “Estimates several measures of DNA sequence variation within and between populations, linkage disequilibrium, recombination, gene flow and gene conversion.” - http://www.ub.es/dnasp/
  • EHH calculator: “Haplotype homozygosity (HH) is an effective measure of linkage disequilibrium (LD) for more than 2 markers.” - http://ihg.gsf.de/cgi-bin/mueller/webehh.pl
  • Entropy-based LD: “Assessment of LD with regard to the sequence, not a particular haplotype. A single quantity summarizes the LD status of the sequence. No emphasis on a particular source of LD such as absent recombination as seen for the pairwise measure D'. An approximate chi-squared test of the significance of the deviation from linkage equilibrium is estimated by a related quantity. The Normalized Entropy Difference, ε can be regarded as a multilocus extension of the commonly used pairwise LD measure r² (Δ²)” - http://capella.uni-kiel.de/eld/eld.htm
  • ETDT: “Uses logistic regression approach to perform TDT for multiallelic markers” - http://www.smd.qmul.ac.uk/statgen/dcurtis/software.html
  • GASSOC: “The program "gassoc" (for genetic association tests) is a program for computing general score tests to test for linkage (in the presence of linkage disequilibrium - LD) between multiallelic genetic markers and disease, when diseased subjects (cases) and their parents are sampled.” - http://iubio.bio.indiana.edu:7780/archive/00000632/
  • GDA: “Computes linkage and hardy-weinberg disequilibrium, some genetic distances, and provides method-of-moments estimators for hierarchical F-statistics.” - http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php
  • GENEPOP on the web: “GENEPOP is a population genetics software package which includes computations for Hardy-Weinberg equilibrium, population differentiation, and genotypic disequilibrium among pairs of loci  - http://wbiomed.curtin.edu.au/genepop/
  • GENETIX: “This set of programs computes several basic parameters of population genetics such as Nei's D and H, Wright's F-statistics (the Weir-Cockerham's and Robertson-Hill's estimators), and linkage disequilibrium D according to Black & Krafsur.” - http://www.univ-montp2.fr/%7Egenetix/genetix/genetix.htm
  • GOLD package: “A software package that provides a graphical summary of linkage disequilibrium in human genetic data” - http://www.sph.umich.edu/csg/abecasis/GOLD/
  • HapGraph and GMEst: “HapGraph is an interactive program for running a simulated annealing search to fit a graphical model for linkage disequilibrium to haplotype data.” - http://episun7.med.utah.edu/~alun/hapgraph/
  • Haploview: “Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.” - http://www.broad.mit.edu/personal/jcbarret/haplo/index.php
  • LDhat: “A package for coalescent analysis of patterns of linkage disequilibrium and estimation of the population recombination rate” - http://www.stats.ox.ac.uk/~mcvean/LDhat/LDhat1.0/LDhat1.0.html
  • LDMAP: “LDMAP is a program for constructing linkage disequilibrium (LD) maps. LD maps are scaled in linkage disequilibrium units (LDUs) and show (when plotted against the physical map) a pattern of plateaus (reflecting regions of low haplotype diversity or 'LD blocks') and steps (which represent recombination hot-spots or recombination events). The LD map has a number of compelling advantages for disease mapping over both the sequence-based physical map and the, often low resolution, genetic linkage map.” - http://cedar.genetics.soton.ac.uk/public_html/helpld.html
  • MIDAS - A software package (MIDAS - Multiallelic Interallelic Disequilibrium Analysis Software) for the estimation and graphical display of interallelic linkage disequilibrium. Linkage disequilibrium is analysed for each allelic combination (of one allele from each of two loci), between all pairwise combinations of any type of multiallelic loci in a contig (or any set) of many loci (including single nucleotide polymorphisms, microsatellites, minisatellites and haplotypes). Data are presented graphically in a novel and informative way, and can also be exported in tabular form for other analyses. This approach facilitates visualisation of patterns of linkage disequilibrium across genomic regions, analysis of the relationships between different alleles of multiallelic markers and inferences about patterns of evolution and selection. MIDAS is a linkage disequilibrium analysis program with a comprehensive graphical user interface providing novel views of patterns of linkage disequilibrium between all types of multiallelic and biallelic markers. http://www.genes.org.uk/software/midas
  • MultiLocus: “This program has been written to facilitate analysis of multi-locus population genetic data. In particular, it allows calculation of various genotypic diversity indices, various linkage disequilibrium indices, and a measure of population differentiation, and allows one to search for subpopulations which do not share polymorphisms” - http://www.agapow.net/software/multilocus/
  • PHASE: “Software for haplotype reconstruction, and recombination rate estimation from population data. The program PHASE implements methods for estimating haplotypes from population genotype data” - http://www.stat.washington.edu/stephens/software.html
  • POPGENE: “User-friendly computer freeware for the analysis of genetic variation among and within populations using co-dominant and dominant markers. It computes both comprehensive genetic statistics (e.g., allele frequency, gene diversity, genetic distance, G-statistics, F-statistics) and complex genetic statistics (e.g., gene flow, neutrality tests, linkage disequilibria, multi-locus structure).” - http://www.ualberta.ca/~fyeh/
  • QTDT: “Performs association tests and TDT for quantitative traits using a variance components approach” - http://www.sph.umich.edu/csg/abecasis/QTDT/
  • R Project for Statistical Computing: “R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. Many packages for estimation of LD exist under the R environment – search for linkage disequilibrium using the search facility under R Project” - http://www.r-project.org/
  • TDT/S-TDT: “Performs TDT and sib-TDT” - http://genomics.med.upenn.edu/spielman/TDT.htm
  • TRIMHAP: “Shared haplotype analysis for estimation of disease gene location” - http://www.vipbg.vcu.edu/trimhap



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