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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://genome.sph.umich.edu/wiki/PedScript

Software tool that allows scripting of simple modifications to pedigree files. (entry from Genetic Analysis Software)

Proper citation: PEDSCRIPT (RRID:SCR_004571) Copy   

•   Source: SciCrunch Registry

http://www.chg.duke.edu/software/pedplot.html

Pedigree Plotting Program for the Pedfile Format (entry from Genetic Analysis Software)

Proper citation: PEDPLOT (RRID:SCR_003843) 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

https://varscan.sourceforge.net/

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).

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://watson.hgen.pitt.edu/register/soft_doc.html

Software application that is a faster version of SLINK (entry from Genetic Analysis Software)

Proper citation: FASTSLINK (RRID:SCR_008664) 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

http://www.hpcf.upr.edu/~humberto/software/TkMap/

Software program for drawing genetic maps (entry from Genetic Analysis Software)

Proper citation: TKMAP (RRID:SCR_007457) Copy   

•   Source: SciCrunch Registry

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

A set of Java programs for genetic epidemiology analysis (entry from Genetic Analysis Software)

Proper citation: GENEPI.JAR (RRID:SCR_008782) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ust.hk/SNPHarvester.html

Software tool for detecting epistatic interactions in genome-wide association studies (entry from Genetic Analysis Software)

Proper citation: SNPHARVESTER (RRID:SCR_008536) Copy   

•   Source: SciCrunch Registry

http://www.simedic.com.ar/bdgen.htm

Powerful database software with improvement tools for paternity testing, database searching (like CODIS) and NRC II recommendations based formulae for investigating likelyhood ratios in putative contributors to crime evidences. Additional genetic population parameters estimations are added in this version. Only spanish version available. (entry from Genetic Analysis Software)

Proper citation: BDGEN (RRID:SCR_008811) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html

FASTLINK is significantly modified and improved version of main programs of LINKAGE that runs much faster sequentially, can run in parallel, allows the user to recover gracefully from a computer crash, and provides abundant new documentation.

Proper citation: FASTLINK (RRID:SCR_007042) Copy   

•   Source: SciCrunch Registry

https://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html

Software application allowing to simulate population genetics datasets. It allows generating genetic data for haploid, diploid, and haplodiploid organisms under a variety of mating systems. It includes various migration and mutation models. Output can be generated for the FSTAT, GENEPOP, and ARLEQUIN genetic analysis packages. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EASYPOP (RRID:SCR_008961) Copy   

•   Source: SciCrunch Registry

http://www.inra.fr/mia/T/CarthaGene/

A genetic/radiation hybrid mapping software that looks for multiple populations maximum likelihood consensus maps using a fast EM algorithm for maximum likelihood estimation and powerful ordering algorithms inspired from TSP (Traveling Salesman Problem) technology. It can handle large data sets made up of different populations (either F2 backcross, recombinant inbred lines, F2 intercross, phase known outbreds, haploid/diploid radiation hybrids). It can also exploit existing syntenic relationships between the organism mapped and a reference (sequenced) organism for accurate dense RH mapping. (entry from Genetic Analysis Software)

Proper citation: CARTHAGENE (RRID:SCR_009013) 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.sph.umich.edu/csg/abecasis/Exact/index.html

Software application for a fast exact Hardy-Weinberg Equilibrium test for SNPs (entry from Genetic Analysis Software)

Proper citation: SNP-HWE (RRID:SCR_008555) Copy   

•   Source: SciCrunch Registry