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http://bios.ugr.es/BMapBuilder/

Software application (entry from Genetic Analysis Software)

Proper citation: BMAPBUILDER (RRID:SCR_007264) Copy   

•   Source: SciCrunch Registry

http://gaow.github.io/genetic-analysis-software/l/linkage---ceph/

Software application (entry from Genetic Analysis Software)

Proper citation: LINKAGE - CEPH (RRID:SCR_007048) Copy   

•   Source: SciCrunch Registry

http://compgen.rutgers.edu/multimap.shtml

Software program for automated construction of genetic maps (entry from Genetic Analysis Software)

Proper citation: MULTIMAP (RRID:SCR_007168) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/thompson/Genepi/MORGAN/Morgan.shtml

Software programs for segregation and linkage analysis, using a variety of Markov chain Monte Carlo (MCMC) methods. Includes MCMC methods for multilocus gene identity by descent (including homozygosity mapping) and Monte Carlo Lod scores. Also, other programs for EM analysis of quantitative traits.

Proper citation: MORGAN (RRID:SCR_006906) Copy   

•   Source: SciCrunch Registry

http://www.pierroton.inra.fr/genetics/labo/Software/Famoz/index.html

Software application that uses likelihood calculation and simulation to perform parentage studies with codominant, dominant, cytoplasmic markers or combinations of the different types (entry from Genetic Analysis Software)

Proper citation: FAMOZ (RRID:SCR_007477) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5th,2023. Software application that uses Monte Carlo method for assessing significance of a case-control association study with multi-allelic marker. (entry from Genetic Analysis Software).

Proper citation: CLUMP (RRID:SCR_007476) Copy   

•   Source: SciCrunch Registry

http://darwin.uvigo.es/software/treescan.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that is intended to provide p-values for the hypothesis of association between evolutionary clades and continuous traits, using haplotype trees. (entry from Genetic Analysis Software)

Proper citation: TREESCAN (RRID:SCR_007108) Copy   

•   Source: SciCrunch Registry

http://pngu.mgh.harvard.edu/purcell/whap/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 24, 2015. This package is no longer supported. The majority of the functionality for conditional haplotype tests in population-based samples has been implemented in PLINK, with a better interface and more robust, faster computation: please use that from now on. Software tool to perform haplotype-based association analysis, for quantitative and qualitative traits, in population and family samples, using single nucleotide polymorphism or multiallelic marker data. What whap can do: * Analyze quantitative and qualitative traits * Handle unrelated individuals and/or parent-offspring trio data * Perform a regression-based haplotype association test for SNP data * Perform a secondary test based on pairwise haplotype similarity * Phase genotype data using a standard E-M approach, and handle ambiguity in E-M inferred haplotypes * Include covariates and moderator variables * Flexibly constrain effects across haplotypes to tested nested models * Perform a robust within-family test when parental genotypes are present * Analyze multiallelic markers (new) * Use dominant or recessive (new) genetic models (new)

Proper citation: Whap (RRID:SCR_007103) Copy   

•   Source: SciCrunch Registry

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

Software application that identifies likely genotyping errors and mutations for a sib pair in the context of multipoint mapping. (entry from Genetic Analysis Software)

Proper citation: SIBMED (RRID:SCR_007495) Copy   

•   Source: SciCrunch Registry

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

Software application for non-parametric linkage analysis using allele sharing in sib pairs (entry from Genetic Analysis Software)

Proper citation: BETA (RRID:SCR_007556) Copy   

•   Source: SciCrunch Registry

http://www.wesbarris.com/mapcreator/

Software application to create gene maps using either radiation hybrid data or linkage data (entry from Genetic Analysis Software)

Proper citation: MAPCREATOR (RRID:SCR_008001) Copy   

•   Source: SciCrunch Registry

http://www.genetics.emory.edu/labs/epstein/software/scout/index.html

Software program for conducting combined association analysis of triads and unrelated subjects (entry from Genetic Analysis Software)

Proper citation: SCOUT (RRID:SCR_009054) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software for segregation and pathway analysis.

Proper citation: SEGPATH (RRID:SCR_009052) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documetned on May 12,2023. Software application (entry from Genetic Analysis Software)

Proper citation: FASTMAP (2) (RRID:SCR_008635) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application to calculate kinship coefficient or coefficient of coancestry (the probability that alleles at a given locus are identical by descent).

Proper citation: KIN (RRID:SCR_009047) Copy   

•   Source: SciCrunch Registry

http://chgr.mc.vanderbilt.edu/genomeSIMLA/

Software application that is a forward-time population simulation method that can simulate realistic patterns of LD in both family-based and case-control datasets. (entry from Genetic Analysis Software)

Proper citation: GENOMESIMLA (RRID:SCR_008990) Copy   

•   Source: SciCrunch Registry

http://www.genogram.org/

Software application that is a graphic way of organizing the mass of information gathered during a family assessment and finding patterns in the family system (entry from Genetic Analysis Software)

Proper citation: GENOGRAM-MAKER (RRID:SCR_008751) Copy   

•   Source: SciCrunch Registry

http://www.hoschl.cz/faster/

Software application to reduce family members so the families can be used in GENEHUNTER program. FASTER eliminates the most redundant individuals according to the set of weights (preferences) (Age, Information about genetic Markers, etc.) The program has several features such as automatical reducement of branches without any affected individuals, etc. (entry from Genetic Analysis Software)

Proper citation: FASTER (RRID:SCR_009045) Copy   

•   Source: SciCrunch Registry

http://www.multiqtl.com/

Software application that integrates a broad spectrum of data mining, statistical analysis, interactive visualization and modeling tools that allow QTL analysis based on advanced and sophisticated methods for maximum extraction of the mapping information from data. (entry from Genetic Analysis Software)

Proper citation: MULTIQTL (RRID:SCR_009043) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/~mcpeek/software/spermseg

Software application for analysis of segregation in single-sperm data (entry from Genetic Analysis Software)

Proper citation: SPERMSEG (RRID:SCR_009044) Copy   

•   Source: SciCrunch Registry