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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: “Twolocus 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.mrcepid.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/cgibin/mueller/webehh.pl
 Entropybased 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
chisquared 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.unikiel.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 hardyweinberg disequilibrium, some genetic distances, and provides
methodofmoments estimators for hierarchical Fstatistics.”

http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php
 GENEPOP on the web:
“GENEPOP is a population genetics software package which
includes computations for HardyWeinberg 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 Fstatistics (the WeirCockerham's and
RobertsonHill's estimators), and linkage disequilibrium D according to
Black & Krafsur.” 
http://www.univmontp2.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 hotspots or recombination events). The LD map has a
number of compelling advantages for disease mapping over both the
sequencebased 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 multilocus
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:
“Userfriendly computer freeware for the analysis of genetic
variation among and within populations using codominant and dominant
markers. It computes both comprehensive genetic statistics (e.g.,
allele frequency, gene diversity, genetic distance, Gstatistics,
Fstatistics) and complex genetic statistics (e.g., gene flow,
neutrality tests, linkage disequilibria, multilocus
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.rproject.org/
 TDT/STDT: “Performs
TDT and sibTDT” 
http://genomics.med.upenn.edu/spielman/TDT.htm
 TRIMHAP: “Shared
haplotype analysis for estimation of disease gene location” 
http://www.vipbg.vcu.edu/trimhap
