连锁不平衡分析软件

A Compilation of Some Available Software forLinkage Disequilibrium Analysis
Available on/from this site

• MIDAS- interallelic linkage disequilibrium analysis for multiallelic andbiallelic markers with interactive graphical interface.
• CubeX- online web tool for calculation of pairwise linkage disequilibriumusing exact solution.

A range of LDsoftware from different authors (in alphabetical order)

• 2LD: “Two-locus LDcalculator for multiallelic markers including SNPs. It computes anumber linkage disequilibrium statistics (including the variance ofD’ 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 handlemultiple genetic markers and missing data.” - http://www.mrc-epid.cam.ac.uk/Personal/jinghua.zhao/software.htm
• ALLASS: “Estimatescomposite linkage disequilibrium for multilocus data using theMalécot isolation by distance equation” - http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/ALLASS
• ARLEQUIN: “Populationgenetic analysis package that includes haplotype estimation by the EMalgorithm and LD analysis for locus pairs; significance tested bypermutation method" - http://anthro.unige.ch/arlequin/
• CubeX: "online web tool for calculation ofpairwise linkage disequilibrium using exact solution" - http://www.oege.org/software/cubex/
• DISEQ : “Multilocusdisequilibrium estimation program” - http://linkage.rockefeller.edu/soft/diseq.html
• DnaSP: “Estimatesseveral measures of DNA sequence variation within and betweenpopulations, linkage disequilibrium, recombination, gene flow and geneconversion.” - http://www.ub.es/dnasp/
• EHH calculator:“Haplotype homozygosity (HH) is an effective measure oflinkage 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 aparticular haplotype. A single quantity summarizes the LD status of thesequence. No emphasis on a particular source of LD such as absentrecombination as seen for the pairwise measure D'. An approximatechi-squared test of the significance of the deviation from linkageequilibrium is estimated by a related quantity. The Normalized EntropyDifference, ε can be regarded as a multilocus extension ofthe commonly used pairwise LD measure r?(Δ?)” - http://capella.uni-kiel.de/eld/eld.htm
• ETDT: “Uses logisticregression 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 computinggeneral score tests to test for linkage (in the presence of linkagedisequilibrium - LD) between multiallelic genetic markers and disease,when diseased subjects (cases) and their parents aresampled.” - http://iubio.bio.indiana.edu:7780/archive/00000632/
• GDA: “Computes linkageand hardy-weinberg disequilibrium, some genetic distances, and providesmethod-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 whichincludes computations for Hardy-Weinberg equilibrium, populationdifferentiation, and genotypic disequilibrium among pairs of loci - http://wbiomed.curtin.edu.au/genepop/
• GENETIX: “This set ofprograms computes several basic parameters of population genetics suchas Nei's D and H, Wright's F-statistics (the Weir-Cockerham's andRobertson-Hill's estimators), and linkage disequilibrium D according toBlack & Krafsur.” - http://www.univ-montp2.fr/%7Egenetix/genetix/genetix.htm
• GOLD package: “Asoftware package that provides a graphical summary of linkagedisequilibrium in human genetic data” - http://www.sph.umich.edu/csg/abecasis/GOLD/
• HapGraph and GMEst:“HapGraph is an interactive program for running a simulatedannealing search to fit a graphical model for linkage disequilibrium tohaplotype data.” - http://episun7.med.utah.edu/~alun/hapgraph/
• Haploview: “Haploviewis designed to simplify and expedite the process of haplotype analysisby providing a common interface to several tasks relating to suchanalyses.” - http://www.broad.mit.edu/personal/jcbarret/haplo/index.php
• LDhat: “A package forcoalescent analysis of patterns of linkage disequilibrium andestimation of the population recombination rate” - http://www.stats.ox.ac.uk/~mcvean/LDhat/LDhat1.0/LDhat1.0.html
• LDMAP: “LDMAP is aprogram for constructing linkage disequilibrium (LD) maps. LD maps arescaled in linkage disequilibrium units (LDUs) and show (when plottedagainst the physical map) a pattern of plateaus (reflecting regions oflow haplotype diversity or 'LD blocks') and steps (which representrecombination hot-spots or recombination events). The LD map has anumber of compelling advantages for disease mapping over both thesequence-based physical map and the, often low resolution, geneticlinkage map.” - http://cedar.genetics.soton.ac.uk/public_html/helpld.html
• MIDAS - A software package (MIDAS -Multiallelic Interallelic Disequilibrium Analysis Software) for theestimation and graphical display of interalleliclinkage disequilibrium. Linkage disequilibrium is analysed for eachallelic combination (of one allele from each of two loci), between allpairwise combinations of any type of multiallelicloci in a contig (or any set) of many loci (including single nucleotidepolymorphisms, microsatellites, minisatellites and haplotypes). Dataare presented graphically in a novel andinformative way, and can also be exported in tabular form for otheranalyses. This approach facilitates visualisation of patterns oflinkage disequilibrium across genomic regions, analysis of therelationships between different alleles of multiallelic markers andinferences about patterns of evolution and selection. MIDAS is alinkage disequilibrium analysis program with a comprehensive graphicaluser interface providing novel views of patterns of linkagedisequilibrium between all types of multiallelic and biallelic markers. http://www.genes.org.uk/software/midas
• MultiLocus: “Thisprogram has been written to facilitate analysis of multi-locuspopulation genetic data. In particular, it allows calculation ofvarious genotypic diversity indices, various linkage disequilibriumindices, and a measure of population differentiation, and allows one tosearch for subpopulations which do not share polymorphisms” - http://www.agapow.net/software/multilocus/
• PHASE: “Software forhaplotype reconstruction, and recombination rate estimation frompopulation data. The program PHASE implements methods for estimatinghaplotypes from population genotype data” - http://www.stat.washington.edu/stephens/software.html
• POPGENE:“User-friendly computer freeware for the analysis of geneticvariation among and within populations using co-dominant and dominantmarkers. 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-locusstructure).” - http://www.ualberta.ca/~fyeh/
• QTDT: “Performsassociation tests and TDT for quantitative traits using a variancecomponents approach” - http://www.sph.umich.edu/csg/abecasis/QTDT/
• R Project for StatisticalComputing: “R is a free software environment for statisticalcomputing and graphics. It compiles and runs on a wide variety of UNIXplatforms, Windows and MacOS. Many packages for estimation of LD existunder the R environment – search for linkage disequilibriumusing the search facility under R Project” - http://www.r-project.org/
• TDT/S-TDT: “PerformsTDT and sib-TDT” - http://genomics.med.upenn.edu/spielman/TDT.htm
• TRIMHAP: “Sharedhaplotype analysis for estimation of disease gene location” - http://www.vipbg.vcu.edu/trimhap