Tools   Select Another Resource Report Type

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.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May24,2023. Software program that implements the Mantel statistics as proposed by Beckmann et al. (2005) to test for association between genetic markers and phenotypes in case-control studies using haplotype information. The potential value of haplotypes has attracted widespread interest in the mapping of complex traits. Haplotype sharing methods take into account linkage disequilibrium information between multiple markers, and may have good power to detect predisposing genes. We present a new approach based on Mantel statistics for space time clustering, which we developed in order to improve the power of haplotype sharing analysis for gene mapping in complex disease. The new statistic correlates genetic similarity and phenotypic similarity across pairs of haplotypes for case-only and case-control studies. The genetic similarity is measured as the shared length between haplotypes around a putative disease locus. Alternative measures for the phenotypic similarity were implemented. (entry from Genetic Analysis Software)

Proper citation: TOMCAT (RRID:SCR_013120) Copy   

•   Source: SciCrunch Registry

http://dlin.web.unc.edu/software/SCORE-Seq/

A command-line program for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant sites of a gene through a weighted linear combination and then related to disease phenotypes through appropriate regression models. The weights can be constant or dependent on allele frequencies and phenotypes. The association testing is based on score-type statistics. The allele-frequency threshold can be fixed or variable. Statistical significance can be assessed by using asymptotic normal approximation or resampling. The current release covers binary and continuous traits with arbitrary covariates under case-control and cross-sectional sampling. (entry from Genetic Analysis Software)

Proper citation: SCORE-SEQ (RRID:SCR_013121) 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

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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://faculty.washington.edu/browning/presto/presto.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software application that calculates individual inbreeding (F) and average relatedness (AR) coefficients. Additionally, users can compute useful parameters in population genetics such as: the number of ancestors explaining genetic variability; the genetic importance of the herds; F statistics from genealogical information. (entry from Genetic Analysis Software)

Proper citation: ENDOG (RRID:SCR_013289) Copy   

•   Source: SciCrunch Registry

http://www7.inra.fr/mia/T/MendelSoft/

Software application for identifying all Mendelian inconsistencies in complex pedigree data with thousand of individuals, including many loops and several errors. Can also infer missing genotypes. (entry from Genetic Analysis Software)

Proper citation: MENDELSOFT (RRID:SCR_013177) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/beaglecall/beaglecall.html

Software package for simultaneous genotype calling and haplotype phasing for unrelated individuals. BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes. BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes. BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation. (entry from Genetic Analysis Software)

Proper citation: BEAGLECALL (RRID:SCR_013301) Copy   

•   Source: SciCrunch Registry

http://dlin.web.unc.edu/software/spreg-2/

Software program for performing regression analysis of secondary phenotype data in case-control association studies. Secondary phenotypes are quantitative or qualitative traits other than the case-control status. Because the case-control sample is not a random sample of the general population, standard statistical analysis of secondary phenotype data can yield very misleading results. SPREG implements valid and efficient statistical methods. (entry from Genetic Analysis Software)

Proper citation: SPREG (RRID:SCR_013261) Copy   

•   Source: SciCrunch Registry

http://biomath.med.uth.gr

Software application for performing genome scan meta-analysis, a quantitative method to identify genetic regions (bins) with consistently increased linkage score across multiple genome scans, and for testing the heterogeneity of the results of each bin across scans. The program provides as an output the average of ranks and three heterogeneity statistics, as well as corresponding significance levels. (entry from Genetic Analysis Software)

Proper citation: HEGESMA (RRID:SCR_013304) Copy   

•   Source: SciCrunch Registry