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http://www.stat.washington.edu/thompson/Genepi/Eclipse.shtml

A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software)

Proper citation: ECLIPSE (RRID:SCR_013130) Copy   

•   Source: SciCrunch Registry

http://csg.sph.umich.edu//abecasis/GRR/

A graphical tool designed for detection of errors in relationship specification in general pedigrees by use of genome scan marker data. (entry from Genetic Analysis Software)

Proper citation: GRR (RRID:SCR_013496) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/thompson/Genepi/Pedfiddler.shtml

Software suite of six programs that can be used as a stand-alone extension of the pedigree drawing facilities found in the publicly available version of PEDPACK. (entry from Genetic Analysis Software)

Proper citation: PEDFIDDLER (RRID:SCR_013376) Copy   

•   Source: SciCrunch Registry

http://pga.gs.washington.edu/VG2.html

Software program that presents complete raw datasets of individuals'' genotype data using a display format with samples as rows and polymorphisms as columns. The color code is: (1) blue: homozygous genotype for the common allele; (2) red: heterozygous genotype; (3) yellow: homozygous genotype for the rare allele; and (4) grey: missing data (entry from Genetic Analysis Software)

Proper citation: VG (RRID:SCR_013378) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/~lin/software/tagIMPUTE/

A command-line program for the imputation of untyped SNPs. tagIMPUTE is based on a few flanking SNPs that can optimally predict the SNP under imputation. (entry from Genetic Analysis Software)

Proper citation: TAGIMPUTE (RRID:SCR_013338) Copy   

•   Source: SciCrunch Registry

http://www.dynacom.co.jp/u-tokyo.ac.jp/snphitlink/

Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (entry from Genetic Analysis Software)

Proper citation: SNP HITLINK (RRID:SCR_013340) Copy   

•   Source: SciCrunch Registry

http://software.bfh-inst2.de/download3.html

Software application (entry from Genetic Analysis Software)

Proper citation: SGS (RRID:SCR_013460) Copy   

•   Source: SciCrunch Registry

http://www.helsinki.fi/~tsjuntun/autoscan/

A helper program to automate the tedious process of the creation of input files from genotype data of genome-wide scans (entry from Genetic Analysis Software)

Proper citation: AUTOSCAN (RRID:SCR_013510) Copy   

•   Source: SciCrunch Registry

http://www2.ujf-grenoble.fr/leca/membres/manel.html

Software application for parentage inference using molecular data from diploid codominant markers (entry from Genetic Analysis Software)

Proper citation: PARENTE (RRID:SCR_004717) Copy   

•   Source: SciCrunch Registry

http://ftp://morgan.med.utah.edu/pub/Mim

Software application using multipoint IBD method for partitioning genetic variance of quantitative traits to specific chromosome regions using data on nuclear families. (entry from Genetic Analysis Software)

Proper citation: Multipoint Identical-by-descent Method (RRID:SCR_004676) Copy   

•   Source: SciCrunch Registry

http://www.mds.qmw.ac.uk/statgen/dcurtis/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A pedigree drawing program using LINKAGE data files (entry from Genetic Analysis Software)

Proper citation: PEDRAW/WPEDRAW (RRID:SCR_004797) Copy   

•   Source: SciCrunch Registry

http://biostatistics.mdanderson.org/SoftwareDownload/

Software application for power and sample-size calculations for the TDT and ASP tests under a wide variety of ascertainment schemes. Uses the flexible genetic model of McGinnis. Most calculations are exact rather than asymptotic. (entry from Genetic Analysis Software)

Proper citation: TDTASP (RRID:SCR_004943) Copy   

•   Source: SciCrunch Registry

http://genomics.med.upenn.edu/spielman/TDT.htm

Software program that provides separate results for TDT, S-TDT, and the combined (overall) test, as appropriate. (entry from Genetic Analysis Software)

Proper citation: TDT/S-TDT (RRID:SCR_005548) Copy   

•   Source: SciCrunch Registry

http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi

Software 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. (entry from Genetic Analysis Software)

Proper citation: HAPLOBLOCKFINDER (RRID:SCR_005844) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/%7Emarchini/software.html

An R package that specifically focuses on statistical and population genetics methods. The motivation behind the package is to produce an easy to use interface to many of the commonly used methods and models used in statistical and population genetics and an alternative interface for some of the methodology produced by our group. (entry from Genetic Analysis Software)

Proper citation: POPGEN (RRID:SCR_007315) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/hapmixmap/hapmixmap_manual.html

Software application for modelling extended haplotypes in genetic association studies, similar to the FASTPHASE program. (entry from Genetic Analysis Software)

Proper citation: HAPMIXMAP (RRID:SCR_006066) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/~mcvean/LDhat/

Software package for the analysis of recombination rates from population genetic data (entry from Genetic Analysis Software)

Proper citation: LDHAT (RRID:SCR_006298) Copy   

•   Source: SciCrunch Registry

http://tvap.genome.wustl.edu/tools/varscan/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: VARSCAN (RRID:SCR_006849) Copy   

•   Source: SciCrunch Registry

The record is no longer available at this source.

Software application that is part of the LINKAGE auxiliary programs (entry from Genetic Analysis Software)

Proper citation: LSP (RRID:SCR_007059) Copy   

•   Source: SciCrunch Registry

http://bios.ugr.es/~mabad/rTDT/index.html

Software application (entry from Genetic Analysis Software)

Proper citation: RTDT (RRID:SCR_007336) Copy   

•   Source: SciCrunch Registry