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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   

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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   

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

Software application (entry from Genetic Analysis Software)

Proper citation: HAPBLOCK 2 (RRID:SCR_012788) Copy   

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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   

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https://www.dynacom.co.jp/english/product/snpalyze_e/

Software application (entry from Genetic Analysis Software)

Proper citation: SNPALYZE (RRID:SCR_009401) Copy   

•   Source: SciCrunch Registry

https://www.wur.nl/en/show/SMOOTH.htm

Software tool that recognises and removes the most unrealistic data pointsfor the construction of accurate linkage maps, which is not so much depending on the quality of the mapping software, but mostly on the marker data quality. Missing values and scoring errors can severely influence the calculated marker order. This software was used to construct the 10,000 marker potato map. The removal of improbable data point is a good medicine for linkage maps, that is not easily overdosed. One error is more harmfull than ten missing values. The software was never intended as user-friendly software. In these days it would be more useful to re-do the programming of the pascal source code into a perl script. Anyone who takes the initiative to generate such a script is welcomed to contact the authors. SMOOTH works best in close cooperation with mapping algorithm RECORD (entry from Genetic Analysis Software)

Proper citation: SMOOTH (RRID:SCR_009398) Copy   

•   Source: SciCrunch Registry

http://www.jurgott.org/linkage/simulate.html

Software program to simulate genotypes in family members for a map of linked markers unlinked to a given affection status locus. the output is ready for analysis with UNKNOWN, ISIM, LSIM, or MSIM of the SLINK package. (entry from Genetic Analysis Software)

Proper citation: SIMULATE (RRID:SCR_009391) Copy   

•   Source: SciCrunch Registry

http://simupop.sourceforge.net

A forward-based population genetics simulation program capable of simulating very complex evolution processes on large (think of millions) populations. Major features include variable population size; many built-in and hybrid (write in python) mutation, migration, selection models. simuPOP can be extended in Python so there is no limit on what you can do with it. (entry from Genetic Analysis Software)

Proper citation: SIMUPOP (RRID:SCR_009392) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/yli/whait/

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

Proper citation: WHAIT (RRID:SCR_009425) Copy   

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http://www.molecular-haplotype.org/zaplo/zaplo_index.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016.

Proper citation: ZAPLO (RRID:SCR_009426) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: UNKNOWN (RRID:SCR_009423) Copy   

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http://www.marksgeneticsoftware.net/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that calculates descriptive statistics, genetic distances, and F-statistics. It also performs tests for Hardy-Weinberg equilibrium, exact tests for genetic differentiation, Mantel tests, and UPGMA cluster analyses. (entry from Genetic Analysis Software)

Proper citation: TFPGA (RRID:SCR_009421) Copy   

•   Source: SciCrunch Registry

http://www.stat.ohio-state.edu/~statgen/SOFTWARE/SIMPLE/

Software application that calculates linkage statistics, such as lod scores and NPL statistics by Sequential Imputation. (entry from Genetic Analysis Software)

Proper citation: SIMPLE (RRID:SCR_009389) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/em/em.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program.

Proper citation: EM-DECODER (RRID:SCR_000023) Copy   

•   Source: SciCrunch Registry

Issue

https://cran.r-project.org/web/packages/adegenet/index.html

Software package dedicated to the handling of molecular marker data for multivariate analysis. This package is related to ADE4, a R package for multivariate analysis, graphics, phylogeny and spatial analysis. (entry from Genetic Analysis Software)

Proper citation: ADEGENET (RRID:SCR_000825) Copy   

•   Source: SciCrunch Registry

http://gusevlab.org/projects/germline/

Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERMLINE (RRID:SCR_001720) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/olorin

An interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees. It integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets. (entry from Genetic Analysis Software)

Proper citation: OLORIN (RRID:SCR_002015) Copy   

•   Source: SciCrunch Registry

https://sites.pitt.edu/~weeks/docs/SimIBD.html

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

Proper citation: SIMIBD (RRID:SCR_002094) Copy   

•   Source: SciCrunch Registry