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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.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

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://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

http://www.stat.cmu.edu/~roeder/=ettdt/

Software application (entry from Genetic Analysis Software)

Proper citation: ET-TDT (RRID:SCR_007657) Copy   

•   Source: SciCrunch Registry

http://www.cs.cmu.edu/~genome/FAST-MAP.html

Fluorescent allele-calling software toolkit: a computer software for fully automated microsatellite genotyping. (entry from Genetic Analysis Software)

Proper citation: FASTMAP (1) (RRID:SCR_008346) Copy   

•   Source: SciCrunch Registry

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

Software application that treats the disease-associated markers and their interactions via a bayesian partitioning model and computes, via Markov chain Monte Carlo, the posterior probability that each marker set is associated with the disease. (entry from Genetic Analysis Software)

Proper citation: BEAM (RRID:SCR_007258) Copy   

•   Source: SciCrunch Registry

http://droog.gs.washington.edu/ldSelect.html

Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LDSELECT (RRID:SCR_007010) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A web application and database schema for storing and interactively displaying genetic map data.

Proper citation: INTEGRAYEDMAP (RRID:SCR_007489) Copy   

•   Source: SciCrunch Registry

http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/LDMAP

Software program for constructing linkage disequilibrium (LD) maps. (entry from Genetic Analysis Software)

Proper citation: LDMAP (RRID:SCR_006308) Copy   

•   Source: SciCrunch Registry

http://krunch.med.yale.edu/haplo/

Software application that estimates frequencies of multi-site haplotypes using the EM algorithm (entry from Genetic Analysis Software)

Proper citation: HAPLO 2 (RRID:SCR_009059) Copy   

•   Source: SciCrunch Registry