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POPULATION GENETICS PROGRAMS

ARLEQUIN
*Description (French translation of "Arlecchino", a character of the Italian "Commedia dell'Arte". He has many aspects, but can switch among them very easily according to needs and necessities. Similarly, this software is about the study of genetic polymorphism.) An exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data).
References Schneider S, Kueffer JM, Roessli D, Excoffier L. (1997). Arlequin: A Software for Population Genetic Data Analysis, Version 1.1. Genetics and Biometry Lab, Dept. of Anthropology, Univ Geneva.
Website http://lgb.unige.ch/arlequin/

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DMAP (Disequilibrium MAP)
*Description A composite likelihood model is used to take into account the information from all disease_locus-marker pairs while modeling the variability in the disequilibrium values due to the evolutionary dynamics of the population
Authors Bernie Devlin
References Devlin B, Risch N, Roeder K. (1996). Disequilibrium mapping: composite likelihood for pairwise disequilibrium. Genomics, 36(1):1-16
Website http://wpicr.wpic.pitt.edu/wpiccompgen/

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DMLE (Disease Mapping using Linkage disEquilibrium)
*Description High-resolution mapping of the position of a disease mutation relative to a set of genetic markers using population linkage disequilibrium (LD).
Authors Jeff Reeve, Ying Wang, Rannala (Univ Alberta, Canada)
References Reeve JP, Rannala B. (2002). DMLE+: Bayesian linkage disequilibrium gene mapping. Bioinformatics, 18(6):894-5.
Website http://www.dmle.org/

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GDA (Genetic Data Analysis)
*Description Designed to accompany the second edition of Bruce Weir's book "Genetic Data Analysis" (1996. Sinauer Associates)
Authors Paul Lewis, Dmitri Zaykin
Website http://hydrodictyon.eeb.uconn.edu/people/plewis/software.php

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Genepop on the Web
*Description A website that contains links to Hardy Weinberg Exact test, Linkage Disequilibrium, Population Differentiation, Nm Estimates, Basic Information - allele frequencies, etc., Fst & other correlations, File conversion and Miscellaneous Utilities programs.
Website http://genepop.curtin.edu.au/

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GOLD (Graphical Overview of Linkage Disequilibrium)  
*Description A software package that provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data.
Authors G R Abecasis, William Cookson (Wellcome Trust Centre for Human Genetics, Oxford, UK)
References Abecasis GR, Cookson WO. (2000). GOLD--graphical overview of linkage disequilibrium. Bioinformatics, 16(2):182-3.
Website http://www.sph.umich.edu/csg/abecasis/GOLD/

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LDMAP (Linkage Disequilibrium Map)
**Description LDMAP is a program for constructing linkage disequilibrium (LD) maps. LD maps are scaled in linkage disequilibrium units (LDUs) and often show (when plotted against the physical map) a pattern of plateaus (reflecting perhaps regions of low haplotype diversity or 'LD blocks') and steps (which may represent recombination hot-spots or recombination events). If sufficient data is available (high enough SNP density for covering a region) 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. Unlike the physical map SNP markers should be spaced evenly on the LD map and one LD unit is equivalent to 1 swept radius (representing the extent of useful LD, see below). Uniform SNP spacing on the LD scale is required for coverage of a region or chromosome. LD maps can be constructed automatically from both haplotype and genotype (diplotype) data. It is possible that different populations show the same PATTERN of LD even if the overall LENGTH of the LD map differs (reflecting different population histories). This would be expected to be true if recombination is the major determinant of the LD pattern. Recent evidence suggests quite a close relationship between the pattern of LD and recombination. The LD map may therefore resemble a high-resolution linkage map which will permit more detailed studies of the relationship between recombination and sequence.
Authors Andy Collins
References Online manual
Website http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/LDMAP

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MLD
*Description Performing a shuffling version of the exact conditional tests for different combinations of allelic and genotypic disequilibrium on haploid
Authors Dmitri Zaykin
References Zaykin D, Zhivotovsky L, Weir BS. (1995). Exact tests for association between alleles at arbitrary numbers of loci. Genetica, 96(1-2):169-78.
Website ftp://statgen.ncsu.edu/pub/zaykin/

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* Description retrieved from http://linkage.rockefeller.edu/soft/
** Description retrieved from http://cedar.genetics.soton.ac.uk/public_html/helpld.html