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http://www.biometris.wur.nl/uk/Software/MapChart/

Software application that produces charts of genetic linkage and QTL data. The charts are composed of a sequence of vertical bars representing the linkage groups or chromosomes. On these bars the positions of loci are indicated, and next to the bars QTL intervals and QTL graphs can be shown. MapChart reads the linkage information (i.e. the locus and QTL names and their positions) from text files. Many options to adapt the charts to different purposes. Can produce graphic files (enhanced windows metafile format) which can be enhanced with other MS-Windows software. (entry from Genetic Analysis Software)

Proper citation: MAPCHART (RRID:SCR_009273) Copy   

•   Source: SciCrunch Registry

http://polymorphism.ucsd.edu/cgi-bin/PRL/mama/mama.cgi

Software application (entry from Genetic Analysis Software)

Proper citation: MAMA (RRID:SCR_009270) Copy   

•   Source: SciCrunch Registry

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

Suite of Python scripts for quality control of genetic markers, group analysis and inference of linear order of markers on linkage groups. MadMapper_RECBIT analyses raw marker scores for recombinant inbred lines. MadMapper_RECBIT generates pairwise distance scores for all markers, clusters based on pairwise distances, identifies genetic bins, assigns new markers to known linkage groups, validates allele calls, and assigns quality classes to each marker based on several criteria and cutoff values. MadMapper_XDELTA utilizes new algorithm, Minimum Entropy Approach and Best-Fit Extension, to infer linear order of markers. MadMapper_XDELTA analyzes two-dimensional matrices of all pairwise scores and finds best map that has minimal total sum of differences between adjacent cells (map with lowest entropy). MadMapper is freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software)

Proper citation: MADMAPPER (RRID:SCR_009267) Copy   

•   Source: SciCrunch Registry

http://cogent.iop.kcl.ac.uk/MaGIC.cogx

Software program to generate targeted marker sets for genome-wide association studies.

Proper citation: Marker And Gene Interpolation and Correlation (RRID:SCR_009268) Copy   

•   Source: SciCrunch Registry

http://www.hsph.harvard.edu/faculty/alkes-price/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. A software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power. LTSOFT employs a liability threshold model approach that takes advantage of known epidemiological results to better model the covariates'' relationship to the phenotype of interest (entry from Genetic Analysis Software)

Proper citation: LTSOFT (RRID:SCR_009266) Copy   

•   Source: SciCrunch Registry

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

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

Proper citation: LRP (RRID:SCR_009263) Copy   

•   Source: SciCrunch Registry

http://statgen.iop.kcl.ac.uk/lpop/

Software application that detects population stratification in samples of unrelated individuals for whom a number of unlinked genotypes have been measured. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: L-POP (RRID:SCR_009262) Copy   

•   Source: SciCrunch Registry

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

Software program for analyses a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci. (entry from Genetic Analysis Software)

Proper citation: LOKI (RRID:SCR_009260) Copy   

•   Source: SciCrunch Registry

http://www.molecular-haplotype.org/profiler/profiler_intro.htm

A flexible software tool to generate the probability distribution of joint multilocus genotypes defined by sets of individuals within the pedigree and sets of markers within the framework map. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PROFILER (RRID:SCR_009339) Copy   

•   Source: SciCrunch Registry

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

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

Proper citation: PREPLINK (RRID:SCR_009335) Copy   

•   Source: SciCrunch Registry

http://fisher.utstat.toronto.edu/sun/Software/Prest or previously, http://galton.uchicago.edu/~mcpeek/software/prest

Software program that detects pedigree errors in general outbred pedigrees by use of genome-screen data. When a potential pedigree error is detected, our companion program, ALTERTEST, determines which relationships are compatible with the observed genotype data. Both programs are freely available on the web. (entry from Genetic Analysis Software)

Proper citation: PREST (RRID:SCR_009336) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Excel spreadsheet to calculate power of affected sibpairs and TDT analyses (entry from Genetic Analysis Software)

Proper citation: POWTEST (RRID:SCR_009334) Copy   

•   Source: SciCrunch Registry

http://www.geneticepi.com/Research/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: POOL STR (RRID:SCR_009331) Copy   

•   Source: SciCrunch Registry

http://alla.cs.gsu.edu/~software/tagging/tagging.html

Software application that can be used for tagging SNP selection and genotype prediction (entry from Genetic Analysis Software)

Proper citation: MLR-TAGGING (RRID:SCR_009299) Copy   

•   Source: SciCrunch Registry

http://statgen.ncsu.edu/powermarker/

A comprehensive set of statistical methods for genetic marker data analysis, designed especially for SSR/SNP data analysis. PowerMarker builds a powerful user interface around both new and traditional statistical methods for population genetic analysis. See analysis to check out the versatility of PowerMarker. PowerMarker is also a 2D Viewer - which was used intensively for visualizing linkage disequilibria results. (entry from Genetic Analysis Software)

Proper citation: POWERMARKER (RRID:SCR_009332) Copy   

•   Source: SciCrunch Registry

http://www.emboss.co.nz/products.php?pid=2

Software application to draw chromosome maps from the output of MAPMAKER/EXP. The output format is a Enhanced Metafile, which can be imported into most Windows-based presentation or document editing programs. (entry from Genetic Analysis Software)

Proper citation: MMDRAWER (RRID:SCR_009296) Copy   

•   Source: SciCrunch Registry

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

Software application for complex segregation analysis with the mixed model (major locus and polygenes). (entry from Genetic Analysis Software)

Proper citation: POINTER (RRID:SCR_009330) Copy   

•   Source: SciCrunch Registry

http://www.imbs.uni-luebeck.de/pub/minsage/index.html

Software application to calculate the sample size of genotypes minimally required to ensure that all alleles with a specified frequency at one locus are detected with a given confidence (entry from Genetic Analysis Software)

Proper citation: MINSAGE (RRID:SCR_009293) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/stephens/software.html

Software program that implements a new statistical method for reconstructing haplotypes from population genotype data (entry from Genetic Analysis Software)

Proper citation: PHASE (RRID:SCR_009327) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,20023. Software application for identifying all Mendelian inconsistencies in pedigree data. (entry from Genetic Analysis Software)

Proper citation: PEDCHECK (RRID:SCR_009322) Copy   

•   Source: SciCrunch Registry