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http://csg.sph.umich.edu/boehnke/p_act.php

An R program that adjusts sets of up to 1000 p-values from association tests between correlated traits and SNPs for multiple testing, accounting for the correlation between tests. (entry from Genetic Analysis Software)

Proper citation: P ACT (RRID:SCR_009314) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/margarita/

Software application that infers genealogies from population genotype data and uses these to map disease loci. These genealogies take the form of the Ancestral Recombination Graph (ARG). The ARG defines a genealogical tree for each locus, and as one moves along the chromosome the topologies of consecutive trees shift according to the impact of historical recombination events. (entry from Genetic Analysis Software)

Proper citation: MARGARITA (RRID:SCR_009279) Copy   

•   Source: SciCrunch Registry

http://www.dpw.wau.nl/pv/PUB/MapComp/

Software application that can be used to compare linkage maps obtained from different sources/populations/etc.. It will draw the linkage maps and look for common marker names, these are then connected in the drawing with dashed lines. All neighboring maps are compared in this way. Images can be printed and saved. Orders of the MAPs (ie which map is compared with which other map) can be changed and maps can be flipped (right mouse button). remark: MapComp bears close relationships with the GGT software package (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAPINSPECT (RRID:SCR_009277) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/n-1.html#nocom

Software application to estimate parameters for mixture of normal distributions (entry from Genetic Analysis Software)

Proper citation: NOCOM (RRID:SCR_009310) Copy   

•   Source: SciCrunch Registry

http://mapdisto.free.fr/

Software program for mapping genetic markers in experimental segregating populations like backcross, doubled haploids, single-seed descent. Its specificity is to propose recombination fraction estimates in case of segregation distortion. It can (1) compute and draw genetic maps easily and quickly through a graphical interface; (2) facilitate the analysis of marker data showing segregation distortion due to differential viability of gametes or zygotes. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MAPDISTO (RRID:SCR_009275) Copy   

•   Source: SciCrunch Registry

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

Software application for multiple pairwise linkage analysis under interference (entry from Genetic Analysis Software)

Proper citation: MAP/MAP+/MAP+H/MAP2000 (RRID:SCR_009272) Copy   

•   Source: SciCrunch Registry

http://www.marksgeneticsoftware.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that tests for population structure through the use of Mantel tests (entry from Genetic Analysis Software)

Proper citation: MANTEL-STRUCT (RRID:SCR_009271) Copy   

•   Source: SciCrunch Registry

http://www.biology.duke.edu/noorlab/multsim.html

Software application to analyze the numbers of individuals that founded new populations following a bottleneck or founding event (entry from Genetic Analysis Software)

Proper citation: MULTISIM (RRID:SCR_009308) Copy   

•   Source: SciCrunch Registry

http://pritch.bsd.uchicago.edu/software/maldsoft_download.html

Software program for admixture mapping of complex trait loci, using case-control data. The samples should come from a recently-admixed population; additional ''learning'' samples from the parental populations are helpful. (entry from Genetic Analysis Software)

Proper citation: MALDSOFT (RRID:SCR_009269) Copy   

•   Source: SciCrunch Registry

http://darwin.cwru.edu/sage/

Software application that provides researchers with the tools necessary for various types of statistical genetic analysis of human family data. (entry from Genetic Analysis Software)

Proper citation: SAGE (RRID:SCR_009302) Copy   

•   Source: SciCrunch Registry

http://www-genome.wi.mit.edu/ftp/distribution/software/pedmanager/

Software application (entry from Genetic Analysis Software)

Proper citation: PEDMANAGER (RRID:SCR_009300) Copy   

•   Source: SciCrunch Registry

http://ftp://linkage.rockefeller.edu/software/lrtae/

Software application to compute a likelihood ratio test statistic that increases power to detect genetic association in the presence of phenotype, genotype, and/or haplotype misclassification errors. In addition, the program produces asymptotically unbiased estimates of frequency parameters. (entry from Genetic Analysis Software)

Proper citation: LRTAE (RRID:SCR_009265) Copy   

•   Source: SciCrunch Registry

http://c2s2.yale.edu/software/lot/

Software application (entry from Genetic Analysis Software)

Proper citation: LOT (RRID:SCR_009261) Copy   

•   Source: SciCrunch Registry

http://archive.broadinstitute.org/mpg/tagger/

Software application (entry from Genetic Analysis Software)

Proper citation: TAGGER (RRID:SCR_009419) Copy   

•   Source: SciCrunch Registry

https://watson.hgen.pitt.edu/docs/splink108.html

Software application for linkage analysis using affected sib pairs (entry from Genetic Analysis Software)

Proper citation: SPLINK (RRID:SCR_009414) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/ssahasnp-0

A polymorphism detection tool that detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. For those less repetitive or non-repetitive reads, we place them uniquely on the reference genome sequence and find the best alignment according to the pair-wise alignment score if there are multiple seeded regions. From the best alignment, SNP candidates are screened, taking into account the quality value of the bases with variation as well as the quality values in the neighbouring bases, using neighbourhood quality standard (NQS). For insertions/deletions, we check if the same indel is mapped by more than one read, ensuring the detected indel with high confidence. (entry from Genetic Analysis Software)

Proper citation: SSAHASNP (RRID:SCR_009415) Copy   

•   Source: SciCrunch Registry

http://www.maths.lancs.ac.uk/~fearnhea/Hotspot/

Software program that analyzes sequence data. It obtains an approximation to the likelihood of a summary of the data (as such it can be thought of as a marginal likelihood approach). It does not use all the information in the data, but computationally it can be substantially more efficient than the full-likelihood methods (and hence able to analyze larger data sets). (entry from Genetic Analysis Software)

Proper citation: SEQUENCE LD/SEQUENCE LDHOT (RRID:SCR_009379) Copy   

•   Source: SciCrunch Registry

https://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program for fast calculation of empirical and adjusted p-values for correlated and uncorrelated hypotheses in multiple testing experiments. It is based on the Free Step-Down Resampling Method for controlling the Family Wise Error Rate, originally proposed by Westfall and Young (1993), and implements a variation of the efficient algorithm of Ge et al. (2003), in which the originally necessary re-sampling effort was reduced considerably and the method made computationally more feasible. The program is independent of the underlying test statistic and works with provided observed and permutation test statistics. (entry from Genetic Analysis Software)

Proper citation: SDMINP (RRID:SCR_009377) Copy   

•   Source: SciCrunch Registry

https://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3434

Software application that simulate pedigrees and genetic data in age-structured populations (entry from Genetic Analysis Software)

Proper citation: SPIP (RRID:SCR_009410) Copy   

•   Source: SciCrunch Registry

http://www.joslinresearch.org/LabSites/Krolewski/splat/

Software application that can calculate virtually any linkage test statistic under several sib pair study designs: affected, discordant, unaffected, and pairs defined by threshold values for quantitative traits, such as extreme discordant sib pairs. It uses the EM algorithm to compute maximum likelihood estimates of sharing (subject to any user-specified domain restrictions or null hypotheses) and then plots lod scores versus chromosomal position. It includes a novel grid scanning capability that enables simultaneous visualization of multiple test statistics. Phenotype definitions can be modified without recalculating inheritance vectors, thereby providing considerable analytical flexibility. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPLAT (RRID:SCR_009411) Copy   

•   Source: SciCrunch Registry