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http://www.chgb.org.cn/htSNPer/htSNPer.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Java program for characterizing the haplotype block structure and selecting haplotype tagging SNP (entry from Genetic Analysis Software)

Proper citation: HTSNPER (RRID:SCR_009242) Copy   

•   Source: SciCrunch Registry

http://www.math.mtu.edu/~shuzhang/software.html

Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software)

Proper citation: HS-TDT (RRID:SCR_009240) Copy   

•   Source: SciCrunch Registry

http://www.biomath.medsch.ucla.edu/faculty/klange/software.html

THIS RESOURCE IS NO LOGER IN SERVICE. Documented on May 16,2023. A simple dBASE III program for the management of pedigree and locus data. It permits easy extraction of genetic data for use with MENDEL and FISHER. (entry from Genetic Analysis Software)

Proper citation: DGENE (RRID:SCR_009158) Copy   

•   Source: SciCrunch Registry

http://www.infobiogen.fr/services/CoPE

Software application that includes a Java program for drawing pedigrees and a standardized system for pedigree storage. Unlike other existing pedigree programs, this software is particularly intended for epidemiologists in the sense that it allows customized automatic drawing of large numbers of pedigrees and remote and distributed consultation of pedigrees. (entry from Genetic Analysis Software)

Proper citation: COPE (RRID:SCR_009153) Copy   

•   Source: SciCrunch Registry

https://github.com/gaow/genetic-analysis-software/blob/master/pages/CHROMOSCAN.md

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that is an implementation of a genome-based scan statistic that detects genomic regions.

Proper citation: CHROMOSCAN (RRID:SCR_009151) Copy   

•   Source: SciCrunch Registry

http://innovation.ox.ac.uk/licence-details/chiamo/

Software application for calling genotypes from the Affymetrix 500K Mapping chip. The program allows for multiple cohorts which have potentially different intensity characteristics that can lead to elevated false-positive rates in genome-wide studies. The underlying model has a hierarchical structure that allows for correlation between the parameters of each cohort. The output files produced by CHIAMO feed directly into both the programs SNPTEST and IMPUTE. CHIAMO was used to call genotypes for the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC).

Proper citation: CHIAMO (RRID:SCR_009150) Copy   

•   Source: SciCrunch Registry

http://www.atgc.org/XLinkage/

Software application that serves as a visualization tool to validate constructed genetic maps. CheckMatrix generates graphical genotypes and two-dimensional heat plots of pairwise scores. Visualization of regions with positive and negative linkage as well as of allele fraction per marker simplifies genetic map validation without applying statistical approaches. CheckMatrix works in conjunction with MadMapper and freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software)

Proper citation: CHECKMATRIX (RRID:SCR_009149) Copy   

•   Source: SciCrunch Registry

http://www.uoguelph.ca/~rdanzman/software/PROBMAX/

Software application for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny (entry from Genetic Analysis Software)

Proper citation: PROBMAX (RRID:SCR_009337) Copy   

•   Source: SciCrunch Registry

http://www.statgen.ucr.edu/software.html

Software application that is a user defined SAS procedure for mapping quantitative trait loci (QTL). Since this procedure is not a built-in SAS procedure, users need to obtain a copy of the executable file of PROC QTL and install the software in their personal computers before PROC QTL can be executed. Of course, users need a regular SAS license prior to the installation of PROC QTL. Once PROC QTL is installed, it can be called just like any other SAS procedures. Users will not notice the differences between this customized procedure and other built-in SAS procedures. (entry from Genetic Analysis Software)

Proper citation: PROC QTL (RRID:SCR_009338) Copy   

•   Source: SciCrunch Registry

http://phg.mc.vanderbilt.edu/content/powertrim

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. Software application that automate the decision to remove objects from a pedigree with a minimum loss information (entry from Genetic Analysis Software)

Proper citation: POWERTRIM (RRID:SCR_009333) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.biomath.jussieu.fr/pub/mlbgh (not available)

Software application that is an extension of the GENEHUNTER program to perform sib-pair and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB) method. (entry from Genetic Analysis Software)

Proper citation: MLBGH (RRID:SCR_009297) Copy   

•   Source: SciCrunch Registry

http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/index.html

Software application (entry from Genetic Analysis Software)

Proper citation: MKGST (RRID:SCR_009295) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Minimac

Software application that is a low memory, computationally efficient implementation of the MaCH algorithm for genotype imputation. It is designed to work on phased genotypes and can handle very large reference panels with hundreds or thousands of haplotypes. The name has two parts. The first, mini, refers to the modest amount of computational resources it requires. The second, mac, is short hand for MaCH, our widely used algorithm for genotype imputation. (entry from Genetic Analysis Software)

Proper citation: MINIMAC (RRID:SCR_009292) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/plem/

Software application (entry from Genetic Analysis Software)

Proper citation: PL-EM (RRID:SCR_009329) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/peer/

Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python.

Proper citation: PEER (RRID:SCR_009326) Copy   

•   Source: SciCrunch Registry

http://www.sfbr.org/sfbr/public/software/pedsys/pedsys.html

Full-scale database system developed as a specialized tool for management of genetic, pedigree and demographic data. (entry from Genetic Analysis Software)

Proper citation: PEDSYS (RRID:SCR_009324) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/Merlin

Software application that carries out single-point and multipoint analyses of pedigree data, including IBD and kinship calculations, nonparametric and variance component linkage analyses, error detection and information content mapping. For multipoint analyses in dense maps, Merlin allows the user to impose constraints on the number of recombinants between consecutive markers. Merlin estimates haplotypes by finding the most likely path of gene flow or by sampling paths of gene flow at all markers jointly. It can also list all possible nonrecombinant haplotypes within short regions. Finally, Merlin provides swap-file support for handling very large numbers of markers as well as gene-dropping simulations for estimating empirical significance levels. (entry from Genetic Analysis Software)

Proper citation: MERLIN (RRID:SCR_009289) Copy   

•   Source: SciCrunch Registry

http://www.genetics.ucla.edu/software/

Software application for genetic analysis of human pedigree data under models involving a small number of loci. MENDEL is useful for segregation analysis, linkage calculations, genetic counseling, allele frequency estimation, and related kinds of problems. (entry from Genetic Analysis Software)

Proper citation: MENDEL (RRID:SCR_009288) Copy   

•   Source: SciCrunch Registry

http://pedagree.free.fr/

Software program for detecting autosomal marker Mendelian incompatibilities in pedigree data (entry from Genetic Analysis Software)

Proper citation: PEDAGREE (RRID:SCR_009321) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that uses as input a trio of files: 1) a LINKAGE-format locus file modified to contain locus name information; 2) a LINKAGE-format pedigree file; and 3) a map file. Mega2 then takes this trio of input files and, via a menu-driven interface, transforms them into various other file formats, thus greatly facilitating a variety of different analyses. In addition, for many of these options, it also sets up a C-shell script that then can automatically run these analyses (if you are using Mega2 in a Unix environment that supports C-shell scripts). (entry from Genetic Analysis Software)

Proper citation: MEGA2 (RRID:SCR_009286) Copy   

•   Source: SciCrunch Registry