1.2 c

2.0

(Need update)

2.3

2.5

L

(Need update)

L

(See Manual

beagle options)

BEAGLE performs haplotype phase inference, missing data inference, single marker association testing, haplotypic association testing, and permutation testing for large scale case-control studies (including GWAS studies.  It can:  phase genotype data (i.e. infer haplotypes);  infer missing genotype data; build a localized haplotype cluster model of the linkage disequilibrium structure;  cluster similar haplotypes at each location in the genome;  test single markers and haplotypes clusters for association with a binary trait;  perform permutation testing to assess statistical significance.

L

1.1

V2

L

blade -h

(Need update)

Bayesian LinkAge DisEquilibrium mapping ;  Reference

CLUSTCC

EDAC power
calculator

Web

See Refs

(Click on Link)

For an extreme-sibpair (ESP) study design using both extremely discordant and concordant (EDAC) sibpairs, this web-based utility calculates necessary #s of various types of extreme sibpairs for a desired power, or power for a given configuration of different types of ESPs. Refer to papers for details. Note that the optimization procedure described in the papers was not implemented in this web calculator. 
PDF Gu C et al Genet Epidemiol 1996 13:513-533;  PDF Gu C et al Genetics 2002 160:1733-1743

FASTLINK

3.0

4.1.P

L

(See Website)

(Need update)

The core of the LINKAGE package is a series of programs for MLE of recombination rates, calculation of lod score tables, and analysis of genetic risks. The analysis programs are divided into two groups. The first group can be used for general pedigrees with marker and disease loci. Programs in the second group are for three-generation families and codominant marker loci, and are primarily intended for the construction of genetic maps from data on reference families.  The input to the LINKAGE programs is divided into pedigree and genotypic data, on the one hand; and locus description, recombination rates, and gene order, on the other. The pedigree and genotypic data must be processed prior to analysis by a series of preparatory programs that accompany the analytic programs in the LINKAGE package.  The LINKAGE package contains additional control programs that provide a "shell," or interface, to facilitate the use of the analytic programs. The control programs are not described here.

fastPHASE

1.1

L

PDF

fastPHASE  

(See Manual)

FBAT

1.5.5

2.0.2

L

Online

fbat151 /

fbat155_linux

(Need update)

Fugue

0.2.3

L

Online

fugue

(See Manual)

(Merlin and QTDT style input)

FUGUE is program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure. Given a query sequence (or a sequence alignment), FUGUE scans a database of structural profiles, calculates the sequence-structure compatibility scores and produces a list of potential homologues and alignments. 

G.A.S.P.

3.33

(See Manual)

a comprehensive package for the management and analysis of pedigree data. it offers: 1. Powerful database management tools, specifically designed for family data; 2. Automatic pedigree drawing; 3. Segregation and linkage analysis, based on traditional maximum likelihood methods and newer, more powerful, Monte Carlo methods that can model both genetic and environmental factors.

GASSOC

1.06

Doc

(See Manual)

Statistical methods for disease and genetic marker associations using cases and their parents. These methods include an extension of the transmission/disequilibrium test (TDT) for multiple marker alleles, as well as additional general tests sensitive to associations that depend on dominant or recessive genetic mechanisms.

Genehunter

2.1.4.3

L

Online

gh /

gh64

multipoint analysis of pedigree data including: non-parametric linkage analysis, LOD-score computation, information-content mapping, haplotype reconstruction.  The gh64 version has been recompiled to allow for > 64 alleles at a given Msat.

Genehunter2

Online

GeneHunter 2 is an extension of the GeneHunter software that provides the researcher with a much wider range of analyses for performing linkage and disequilibrium analyses.  Still a test version?

Genehunter-

Imprinting

1.3

2.1 r3

PDF

ghi

(Need update)

modification of the GENEHUNTER software package (versions 1.3 and 2.1 release 3; Kruglyak et al. 1996; Kruglyak and Lander 1998; Markianos et al. 2001). It allows for a parametric multi-marker linkage analysis of dichotomous traits caused by imprinted genes – that is, of traits showing a parent-of-origin effect. By specification of two heterozygote penetrance parameters, paternal and maternal origin of the disease allele can be treated differently in terms of probability of expression of the trait. Therefore, a disease model which accounts for imprinting includes four penetrances instead of only three.

Genehunter-

Modscore

2.0.1

PDF

ghm

GENEHUNTER-MODSCORE is a further extension of GENEHUNTER-IMPRINTING (as described above). The program is based on the original GENEHUNTER version 2.1 release 6 (Kruglyak et al. 1996; Kruglyak and Lander 1998; Markianos et al. 2001); it can handle autosomal or pseudoautosomal loci. With the option to use sex-specific recombination fractions (please see below), the pseudoautosomal region for which the genetic maps strongly differ between males and females can now be adequately analyzed. GENEHUNTER-MODSCORE allows for a MOD-score analysis, in which parametric LOD scores are maximized over the parameters of the trait model, i.e., the penetrances and disease allele frequency.

Genehunter-

Two Locus

1.3

PDF

ght

GENEHUNTER-TWOLOCUS is a modification of the GENEHUNTER software package version 1.3 (Kruglyak et al. 1996; Kruglyak and Lander 1998). The program performs parametric and nonparametric multi-marker linkage analysis of dichotomous traits with two autosomal diallelic disease loci. It uses two unlinked marker maps with one disease locus linked to each map. Like the single-disease-locus versions GENEHUNTER-IMPRINTING and GENEHUNTER-MODSCORE (please see above), GENEHUNTER-TWOLOCUS allows for a parametric (LOD-score) analysis with imprinting disease models. It can take into account parent-of-origin effects at both loci.

Genehunter-

Plus

GENEHUNTER-PLUS is a modification of the GENEHUNTER software package which produces output files containing the null and conditional distributions of the test statistic (in nullprobs.dat and probs.dat, respectively). These files can then be used as input to the ASM program which incorporates the allele sharing modeling for lodscores and likelihood ratio tests as developed by Kong and Cox (1997).

Shaun Purcell:  Power calculators for various genetic models, including VC TQL linkage for sibships, VC QTL association for sibships, TDT for discrete traits, TDT and parenTDT with ascertainment, case-control for discrete traits, TDT for threshold-selected quantitative traits, case-control for threshold-selected quantitative traits, epistasis, probability function, various miscellaneous utilities. 

Purcell S, Cherny SS, Sham PC. (2003) Genetic Power Calculator: 
design of linkage and association genetic mapping studies of complex 
traits. Bioinformatics, 19(1):149-150.

GERBIL

1.0

2.0

Win
L

gerbil-linux

(Need update)

GERBIL - an algorithm for simultaneously phasing genotypes into haplotypes and block partitioning. GERBIL was shown to be quick and accurate even when applied to many hundreds of individuals.   GERBIL is now distributed as part of GEVALT, Version 2.0 available.  Reference

GHOST

GOLD

1.1.0

L

Online

collect-simwalk2 haploxt / ldmax setup-simwalk2

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.

GRR

alpha

Win

Online

(See manual)

GRR is a Windows-based application for detecting pedigree errors via graphically inspecting the distribution for marker allele sharing among pairs of family members or all pairs of individuals in a study. 

haplo

v.1

2.5

L

hapcha, prodixx

(Need update)

Haplotyping with computation of conditional probabilities; Estimates frequencies of multi-site haplotypes using the EM algorithm ; Version 2.5 in 1998

haploblockfinder

Web

L

HaploBlockFinder is a package for haplotype block identification, visualization and htSNP selection. It can also compare the haplotype block structure with local LD pattern. The program can be either run as a web service, or standalone executables on local machine.

haplore

L

A Program for Haplotype Reconstruction in Pedigrees

haplo.score

1.0.2

L

A suite of S-PLUS routines that can be used to compute score statistics to test associations between haplotypes and a wide variety of traits, including binary, ordinal, quantitative, and Poisson.  haplo.score is NOW is haplo.stat (Version 1.3.1, updated 6/14/2007).

haploview

?

4.0

Online

PDF

(Need update)

IMPUTE

0.3.2

Online

IMPUTE is a program for imputing unobserved genotypes in genome-wide case-control studies based on a set of known haplotypes (like the HapMap Phase II haplotypes)

LAMP

0.0.9

Online

lamp

(Merlin-QTDT format) (See Manual)

LAMP is  for Linkage and Association Modeling in Pedigrees. It uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.

LINKAGE

archive

It is strongly recommended to use FASTLINK (and/or VITESSE)

Loki

2.4.5

L

PDF

PDF-faq

loki, prep, check_het

Loki is a package developed by Simon C. Heath. Loki analyses a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci. The package is based on work originally done at University of Edinburgh, UK, and developed at University of Washington under NIH grant GM-46255, Genetic Epidemiology of Complex Traits.

Lrtae

1.0

L

Doc

lrtae-linux

One of the more vexing problems in association analysis with cases and controls is misclassification error (e.g., a true case is incorrectly labeled as a control or a homozygote genotype 1 1 is labeled as a heterozygote 1 2). Consequences of such misclassifications are a reduction in the power to detect association and biased estimates or parameters such as genotype or haplotype frequencies in cases and controls. These misclassifications are of primary concern for case/control genetic association studies since there is no way to detect such errors in phenotype or genotype data short of repeated sampling (or double-sampling – see below).  We developed a method, the Likelihood Ratio Test Allowing for Errors (LRTae) to treat this problem. The purpose of this software is to compute the LRTae on genotype and phenotype data provided by the user.   PDF-ref1   PDF-ref2

MACH

1.0

L

Online

MACH 1.0 is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Mapmaker / Sibs

archive

L

GENEHUNTER replaces MAPMAKER/SIBS -- for LINKAGE, FASTLINK, MAPMAKER/SIBS and GENEHUNTER
see Nyholt DR. GENEHUNTER: Your 'One-Stop-Shop' for Statistical Genetic Analysis? Human Heredity 2002;53:2-7

Mega2

2.3.r.2

4.0

L

During a linkage analysis project, it can often be quite difficult to get one’s data in the proper format desired by each different computer program. Not only must the data be converted to the proper format, but also the loci must be reordered into their proper order. To address this problem, we created Mega2

Mendel

5.0.1

L

Online

mendel, gregor

Comprehensive Package for Exact Statistical Genetic Analysis of Qualitative and Quantitative Traits.

Merlin

0.10.2

L

Online

(See Manual)

MERLIN uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around (Abecasis et al, 2002).

Morgan

2.8.2

L

Online

Programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits.  NOT CURRENTLY DOWNLOADED

MX

1.47c

1.54a

L

Online

mxlinux

(Need update)

Mx is a combination of a matrix algebra interpreter and a numerical optimizer. It enables exploration of matrix algebra through a variety of operations and functions. There are many built-in fit fuctions to enable structural equation modeling and other types of statistical modeling of data. It offers the fitting fuctions found in commercial software such as LISREL, LISCOMP, EQS and CALIS, along with facilities for maximum likelihood estimation of parameters from missing data structures, under normal theory. Complex 'nonstandard' models are easy to specify. For further general applicability, it allows the user to define their own fit functions, and optimization may be performed subject to linear and nonlinear equality or boundary constraints.

PAP

5.0

6.0

L

PDF

(See Manual)

(Need update)

Pedigree Analysis Package: can perform (1) compute the likelihood of specified parameter values; (2) compute the probability of each genotype for pedigree members; (3) simulate phenotypes for output into files; (4) maximize the likelihood over specified parameters (with or without standard errors); (5) compute the standard errors of parameters for unknown estimates; (6) simulate phenotypes and estimate parameter values; (7) estimate expected lod score; (8) compute a grid of likelihood over one or two parameters. New additions to V5: assortative mating; TDT; additive multi-locus models

PBAT

3.0

3.5

L

Online

pbat  (See Manual)

(Need update)

Power calculation of family-Based Association Tests

PHASE

2.0.2

2.1

Win
L

PHASE

(Need update)

Software for haplotype reconstruction, and estimating missing genotypes from population data.  SEE fastPHASE can handle larger data-sets than PHASE (e.g. hundreds of thousands of markers in thousands of individuals), but does not provide estimates of recombination rates. PHASE provides recombination estimates.  Authors' experiments suggest that haplotype estimates are slightly less accurate than from PHASE, but missing genotype estimates appear to be similar or even slightly better using fastPHASE

Pedcheck

1.1

L

Online

pedcheck_linux

Program for detecting marker typing incompatibilities in pedigree data

Pedsys

2.beta

2.0

L

Online

pedsys

(Need update)

A database system developed as a specialized tool for management of genetic, pedigree and demographic data. It has been designed principally for use with pedigree analysis of either human or non-human subjects. The system supports integrated collection, management and analysis of constantly evolving data sets by investigators in several different laboratories. Although some of the programs are specialized, many are general enough to be used effectively with data of any sort.

PLINK

1.01

L

Online

(See Manual)
(pedstatsq)

PLINK (ONE SYLLABLE) is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. A range of features: data management, summary statistics, population stratification and basic association analysis.

QTDT

2.4

Win
L

Online

(See Manual)

QTDT provides a convenient one-stop interface for family based tests of linkage disequilibrium. The general models described by Abecasis et al. (2000a, b) are supported, and can be used to analyse quantitative or discrete traits in nuclear families, with or without parental genotypes, or extended pedigrees. In addition, QTDT can calculate exact p-values by permutation even when multiple linked polymorphisms are tested. The tests described by Allison (TDTQ5, 1997), Rabinowitz (1997), Monks et al. (1998) and Fulker et al. (1999) are also supported.

FDR Method:  This software takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. A point-and-click interface is now available!   The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant.  A short tutorial on q-values and false discovery rates is provided with the manual.   Various plots are automatically generated, allowing one to make sensible significance cut-offs.  Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software.   The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.

Sage

4.3

5.4.1

L

(See Manual)

(Need update)

Non-Profit Organizations can obtain S.A.G.E. for free. Please contact sage@darwin.cwru.edu for more information.   S.A.G.E. v5.4 is now available --> NOT DOWNLOADED UNDER USUAL SOURCE

SEGPATH

2.0

L

seglinuxphi

General purpose model and a computer program for combined segregation and path analysis (SEGPATH): Automatically creating computer programs from symbolic language model specifications.  Province MA, Rao DC. (1995).  Genetic Epidmiology, 12, 203-219;  A multivariate and multilocus variance components method based upon structural relationships to assess quantitative trait linkage via SEGPATH. Province MA, Rice TK, Borecki IB, Gu C, and Rao DC. (2001).  Genetic Epidemiology, 24(2), 128-138

Simwalk2

2.83

L

Online

simwalk2

SimWalk2 is a statistical genetics computer application for haplotype, parametric linkage, non-parametric linkage (NPL), identity by descent (IBD) and mistyping analyses on any size of pedigree. SimWalk2 uses Markov chain Monte Carlo (MCMC) and simulated annealing algorithms to perform these multipoint analyses.

SNPHAP

1.2.1

1.3

L

Online

snphap

(Need update)

a program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects:  Uses the EM algorith with "trimming" of improbable assignments ;  Allows for missing data at some loci;  Can search for multiple solutions using random starting points;  Includes a Monte Carlo IP algorithm for multiple imputation, allowing uncertainty of solutions to be explored

SOLAR

2.1.4

4.1.5

L

Online

solar214

SOLAR is a flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, SNP association analysis (QTN and QTLD), and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of multiple quantitative and/or discrete traits which may involve multiple loci (oligogenic analysis), dominance effects, household effects, and interactions. SOLAR stands for Sequential Oligogenic Linkage Analysis Routines --> LATEST VERSION IS 4.1.5 -- NEED TO UPDATE

sptdt

??

Structure

2.1

2.2

L

PDF21 PDF22

structure

(Need update)

The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including microsatellites, RFLPs and SNPs. This method was described in an article in Genetics (155: 945-959).  Extensions to the method were published in Genetics 2003 (164:1567-1587). 

tdtae

1.0

L

Online

tdtae.linux

This program computes a likelihood-based transmission disequilibrium test. The data are genotypes on trios (father, mother, affected child) in which random genotyping errors leading to Mendelian inconsistencies may or may not have occurred. This program computes the TDT-AE statistic on all trios (whether Mendelianly consistent or not) and thereby maintains a correct type I error rate in the presence of random genotyping errors.

TRANSMIT

2.5.4

L

Online

transmit

TRANSMIT tests for association between genetic marker and disease by examining the transmission of markers from parents to affected offspring.  The main features which differ from other similar programs are:  1. It can deal with transmission of multi-locus haplotypes, even if phase is unknown, and  2. Parental genotypes may be unknown.

TreeLinkage

0.2

L

Use SAS macro

seglinuxphi

General purpose model and a computer program for combined segregation and path analysis (SEGPATH): Automatically creating computer programs from symbolic language model specifications.  Province MA, Rao DC. (1995).  Genetic Epidmiology, 12, 203-219;  A multivariate and multilocus variance components method based upon structural relationships to assess quantitative trait linkage via SEGPATH. Province MA, Rice TK, Borecki IB, Gu C, and Rao DC. (2001).  Genetic Epidemiology, 24(2), 128-138

Treescan

0.9

See website

TreeScan, version 0.9 is a program to test the association of continuous quantitative characters with a tree of haplotypes. Described in a paper: Templeton, A. R., T. Maxwell, D. Posada, J. H. Stengård, . Boerwinkle, and C. F. Sing. 2005. Tree scanning: a method for using haplotype trees in phenotype/genotype association studies. Genetics 169: 441-453. Treescan is provided in C source code, and also as a DOS and Windows executable or a Mac OS X executable.

UNPHASED

3.0.12

UNPHASED is a versatile application for performing genetic association analysis. Some of more important features are:  Analysis of nuclear families and unrelated subjects, and combinations of the two;  Analysis of discrete or quantitative traits; Maximum likelihood treatment of missing genotype data and uncertain haplotype;  Global association tests and tests of individual haplotypes; Conditioning tests that allow for previous associations of linked loci; Inclusion of information from additional tag markers;  Support for non-genetic covariates including parent-of-origin; Permutation tests allowing for multiple testing.   NEED TO ADD

Vitesse

1.0

L

Online

vitesse2_linux_intel

(Expired, need new cc)

VITESSE is a software package that computes likelihoods with the functionality of the LINKMAP and MLINK programs from LINKAGE. VITESSE uses the novel algorithms of set-recoding and fuzzy inheritance to reduce the number of genotypes needed for exact computation of the likelihood, which accelerates the calculation. It also represents multilocus genotypes locus-by-locus to reduce the memory requirements. The algorithms in VITESSE were developed and coded by Jeff O'Connell at the University of Pittsburgh. Dan Weeks at the University of Pittsburgh and the Wellcome Trust Centre for Human Genetics at Oxford University collaborated

ZAPLO

Online

zaplo2.1

(Expired, need new cc)

Estimating haplotype frequencies of SNPs assuming no recombination.  No documentation available yet.