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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://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://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://csg.sph.umich.edu/boehnke/simlink.php

Software program to estimate the probability (power) of detecting linkage given family history information on a set of identified pedigrees. (entry from Genetic Analysis Software)

Proper citation: SIMLINK (RRID:SCR_009387) Copy   

•   Source: SciCrunch Registry

http://dmpi.duke.edu/simla-simulation-software-version-32

SIMulation program that generates data sets of families for use in Linkage and Association studies. It allows the user flexibility in specifying marker and disease placement, locus heterogeneity, disequilibrium between markers and between markers and disease loci. Output is in the form of a LINKAGE pedigree file and is easily utilized, either directly or with minimal reformatting, as input for various genetic analysis packages (entry from Genetic Analysis Software)

Proper citation: SIMLA (RRID:SCR_009385) Copy   

•   Source: SciCrunch Registry

http://imbs-luebeck.de/imbs/de/node/34

Software application to calculate nominal significance levels and critical LOD scores depending on the length of the investigated region, number of chromosomes, and the cross-over rate. The global significance level as well as the precision of the calculation have to be specified. (entry from Genetic Analysis Software)

Proper citation: SILCLOD (RRID:SCR_009383) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/s-1.html#siberror

Software application that identifies pedigree errors in sibship data. Examples include half siblings, unrelated individuals, identical twins, and parental exclusions. The test statistic is based on the summation of the number of alleles shared by a pair of relatives for a large number of markers and the number of alleles and allele frequencies for those markers. (entry from Genetic Analysis Software)

Proper citation: SIBERROR (RRID:SCR_009380) 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

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

https://plant-breeding.uni-hohenheim.de/software.html#jfmulticontent_c110647-2

Software application (entry from Genetic Analysis Software)

Proper citation: PLABQTL (RRID:SCR_012789) Copy   

•   Source: SciCrunch Registry

http://econpapers.repec.org/software/bocbocode/s438902.htm

Software application (entry from Genetic Analysis Software)

Proper citation: HAPBLOCK 2 (RRID:SCR_012788) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/annovar/

An efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, as well as mouse, worm, fly, yeast and many others). Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, ANNOVAR can perform: 1. gene-based annotation. 2. region-based annotation. 3. filter-based annotation. 4. other functionalities. (entry from Genetic Analysis Software)

Proper citation: ANNOVAR (RRID:SCR_012821) Copy   

•   Source: SciCrunch Registry

https://www.genetics.ucla.edu/software/download?package=4

Software application for analysis of sperm typing data. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPERM (RRID:SCR_009409) Copy   

•   Source: SciCrunch Registry