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

Software application that takes case-control genotype data as input and produces a ranked list of multi-SNP interactions. In particular, the whole genome is first partitioned into multiple short subgenomes and a boosting tree classifier is built for each subgenomes based on multi-SNP interactions and then used to measure the importance of SNPs. The method keeps relatively more important SNPs from all subgenomes and let them compete with each other in the same way at the next level. The competition terminates when the number of selected SNPs is less than the size of a subgenome. (entry from Genetic Analysis Software)

Proper citation: MEGASNPHUNTER (RRID:SCR_009287) Copy   

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http://carlit.toulouse.inra.fr/MCQTL/

Software package to perform QTL mapping in multi-cross designs that allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all them. Moreover, a diallel modelling of the QTL genotypic effects is allowed in multiple related families. Obviously, the analysis of a single cross is also feasible. (entry from Genetic Analysis Software)

Proper citation: MCQTL (RRID:SCR_009285) Copy   

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http://www-genome.wi.mit.edu/genome_software

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: MAPMAKER/QTL (RRID:SCR_009283) Copy   

•   Source: SciCrunch Registry

http://ib.berkeley.edu/labs/slatkin/eriq/software/mdb_web/

Software application using the mimimum description length model to delineate haplotype blocks (entry from Genetic Analysis Software)

Proper citation: MDBLOCKS (RRID:SCR_009280) Copy   

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http://www.biostat.umn.edu/~nali/SoftwareListing.html

Software application that implements the PAC (Products of Approximate Conditional) model for estimating recombination rate (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HOTSPOTTER (RRID:SCR_009238) Copy   

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http://gaow.github.io/genetic-analysis-software/h-1.html#homoghomogm

Software application (entry from Genetic Analysis Software)

Proper citation: HOMOG/HOMOGM (RRID:SCR_009237) Copy   

•   Source: SciCrunch Registry

http://l.web.umkc.edu/liujian/

Software platform that is based on real haplotype data from the HapMap ENCODE project that can simulate heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model. Moreover, both qualitative and quantitative traits can be simulated using additive genetic model with various genetic parameters designated by users. (entry from Genetic Analysis Software)

Proper citation: HAPSIMU (RRID:SCR_009235) Copy   

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http://gaow.github.io/genetic-analysis-software/l-1.html#loginserm_estihaplo

Software application (entry from Genetic Analysis Software)

Proper citation: LOGINSERM ESTIHAPLO (RRID:SCR_009258) Copy   

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http://compgen.rutgers.edu/multimap/

Software application for conversion of LINKAGE format data files to CRI-MAP format (entry from Genetic Analysis Software)

Proper citation: LNKTOCRI (RRID:SCR_009256) Copy   

•   Source: SciCrunch Registry

http://www.ktl.fi/molbio/software/linkbase/index.html

An easy and practical database-program made for researchers who want to connect the genotype data produced by automatic sequencers ( ABI Prism 377 (Perkin Elmer) and ALF (Pharmacia) ) to linkage and sib-pair programs. (entry from Genetic Analysis Software)

Proper citation: LINKBASE (RRID:SCR_009254) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: LIPED (RRID:SCR_009255) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/staff/churchill/labsite/software/Jqtl/index.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A Java GUI for the popular QTL data analysis software R/QTL that provides a flexible and powerful working environment for users to perform a variety of tasks. (entry from Genetic Analysis Software)

Proper citation: J/QTL (RRID:SCR_009250) Copy   

•   Source: SciCrunch Registry

http://balance.med.utah.edu/wiki/index.php/JPSGCS

Software application to address problems in statistical genetics; however, they include several programs and packages that may be more generally useful, for instance, programs to draw and manipulate graphs, simulation programs, and programs to estimate graphical models. (entry from Genetic Analysis Software)

Proper citation: JPSGCS (RRID:SCR_009249) Copy   

•   Source: SciCrunch Registry

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

Software application for non-parametric linkage and association tests primarily for a quantitative trait (entry from Genetic Analysis Software)

Proper citation: NOPAR (RRID:SCR_009246) Copy   

•   Source: SciCrunch Registry

http://statgen.ncsu.edu/zaykin/htr.html

Software application for haplotype association mapping using unrelated individuals; fixed and sliding window analysis; overall tests and tests for individual haplotype effects (entry from Genetic Analysis Software)

Proper citation: HTR (RRID:SCR_009241) Copy   

•   Source: SciCrunch Registry

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

Software analysis program to evaluate evidence of linkage disequilibrium (LD) in general pedigree data. All family data may be used without nullifying the validity of the association test, even when there is more than one affected in a family. The PDT program performs both allele-specific and genotype-specific LD analysis of individual markers. Version 5.1 adds the ability to perform genotype-specific analysis over marker sets. (entry from Genetic Analysis Software)

Proper citation: PDT (RRID:SCR_009319) Copy   

•   Source: SciCrunch Registry

http://www.ibms.sinica.edu.tw/~csjfann/first%20flow/programlist.htm

Software tool for analyses of pooled DNA data (entry from Genetic Analysis Software)

Proper citation: PDA (RRID:SCR_009317) Copy   

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http://cougar.fhcrc.org/software.php

Software application that is a Windows-based system designed for pedigree data management, providing a graphical interface for pedigree construction and output. (entry from Genetic Analysis Software)

Proper citation: PDPSYS (RRID:SCR_009318) Copy   

•   Source: SciCrunch Registry

http://linkage.rockefeller.edu/pawe/

Software application for power and sample size calculations for genetic case-control association studies allowing for errors (entry from Genetic Analysis Software)

Proper citation: PAWE (RRID:SCR_009316) Copy   

•   Source: SciCrunch Registry

http://lbm.ab.a.u-tokyo.ac.jp/software.html

Software programs that allow a user to get results on segregation ratio, linkage test, recombination value, grouping of markers, ordering of markers by metric multidimensional scaling, drawing map and graphical genotype. ALso QTL analysis by interval mapping and ANOVA are possible. (entry from Genetic Analysis Software)

Proper citation: MAPL (RRID:SCR_009278) Copy   

•   Source: SciCrunch Registry