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http://www.progenygenetics.com/

Fully customizable, comprehensive genetic pedigree and clinical data management software including a multi-user relational database with an integrated pedigree drawing component to manage genetic and pedigree data in one database. Manage Pedigrees, Individuals, SNPs, STRs, Samples, Plates, Genotypes and exports to multiple analysis platforms. (entry from Genetic Analysis Software) * LIMS software, providing advanced sample tracking and management (including functionality to generate and record barcodes) and configurable workflows for your specific environment. * Full genotype management gives users the ability to track not only family-based studies, but Whole Genome Association studies containing 1000''s of samples with large arrays.

Proper citation: PROGENY (RRID:SCR_006647) Copy   

•   Source: SciCrunch Registry

http://www.allelix.net

THIS RESOURCE IS NO LONGER IN SERVICE, documented on September 23, 2013. Software application / data analysis service where one can enter the alleles of commonly used STR by clicking the mouse. The algorithm calculates the paternity index and the Essen-Moeller probability of kinship for the deficiency- and the trio case. Everybody can use the network-software online after registering. The usage on the internet is free. Academic users can ask me to unlock an option to display the details (formulas/frequencies etc.) and to have an export-funktion to MS Word. The program is in German and (non-professional) English. An expansion to other languages is easy, if somebody helps us with the translation. For those who are interested to have the software running on their own intranet (for database security reasons) an individual agreement can be found. (entry from Genetic Analysis Software) (German version is: http://www.allelix.de)

Proper citation: ALLELIX (RRID:SCR_009115) Copy   

•   Source: SciCrunch Registry

http://www.biostat.harvard.edu/complab/dchip/snp.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: DCHIP LINKAGE (RRID:SCR_000835) Copy   

•   Source: SciCrunch Registry

http://solar-eclipse-genetics.org

A flexible and extensive software package for genetic variance components analysis, including linkage analysis, quantitative genetic analysis, and covariate screening. Operations are included for calculation of marker-specific or multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary size and complexity, and for linkage analysis of quantitative traits which may involve multiple loci (oligogenic analysis), dominance effects, and epistasis. (entry from Genetic Analysis Software)

Proper citation: SOLAR (RRID:SCR_000850) Copy   

•   Source: SciCrunch Registry

http://www-rcf.usc.edu/~gqian/software.htm (not available)

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

Proper citation: MRH (RRID:SCR_000841) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/pedigraph/

A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles

Proper citation: PEDIGRAPH (RRID:SCR_001938) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. A pedigree drawing program using LINKAGE data files (entry from Genetic Analysis Software)

Proper citation: PEDRAW/WPEDRAW (RRID:SCR_004797) Copy   

•   Source: SciCrunch Registry

http://biostatistics.mdanderson.org/SoftwareDownload/

Software application for power and sample-size calculations for the TDT and ASP tests under a wide variety of ascertainment schemes. Uses the flexible genetic model of McGinnis. Most calculations are exact rather than asymptotic. (entry from Genetic Analysis Software)

Proper citation: TDTASP (RRID:SCR_004943) Copy   

•   Source: SciCrunch Registry

http://genomics.med.upenn.edu/spielman/TDT.htm

Software program that provides separate results for TDT, S-TDT, and the combined (overall) test, as appropriate. (entry from Genetic Analysis Software)

Proper citation: TDT/S-TDT (RRID:SCR_005548) Copy   

•   Source: SciCrunch Registry

http://cgi.uc.edu/cgi-bin/kzhang/haploBlockFinder.cgi

Software package for haplotype block identification, visualization and htSNP selection. It can also compare the haplotype block structure with local LD pattern. The program can be either run as a web service, or standalone executables on local machine. (entry from Genetic Analysis Software)

Proper citation: HAPLOBLOCKFINDER (RRID:SCR_005844) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A web application and database schema for storing and interactively displaying genetic map data.

Proper citation: INTEGRAYEDMAP (RRID:SCR_007489) Copy   

•   Source: SciCrunch Registry

https://dsgweb.wustl.edu/aldi/software/manuals/unphased/Unphased_manual.pdf

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A suite of programs for association analysis of multilocus haplotypes from unphased genotype data. These include TDTPHASE for case-parent trios, COCAPHASE for case/control data, QTPHASE for quantitative traits in unrelateds, PDTPHASE for general pedigrees, and QPDTPHASE for quantitative traits in general pedigrees. Features include global and individual haplotype tests, main effects and conditional tests, grouping of rare haplotypes, pairwise comparisons of haplotype risk, flexible permutation procedures and calculation of LD measures.

Proper citation: UNPHASED (RRID:SCR_009056) Copy   

•   Source: SciCrunch Registry

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

Software application designed for the construction of highly saturated linkage maps, based on BC1, DH, Radiation Hybrid or CP (CrossPollinators) data sets. F2 is not supported. (entry from Genetic Analysis Software)

Proper citation: COMBIN (RRID:SCR_009050) Copy   

•   Source: SciCrunch Registry

http://cmpg.unibe.ch/software/arlequin3/

An exploratory population genetics software environment able to handle large samples of molecular data (RFLPs, DNA sequences, microsatellites), while retaining the capacity of analyzing conventional genetic data (standard multi-locus data or mere allele frequency data). (entry from Genetic Analysis Software)

Proper citation: ARLEQUIN (RRID:SCR_009051) Copy   

•   Source: SciCrunch Registry

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

Conversion programs from LINKAGE files are available. The program uses peeling and can employ nested conditioning. There is an automatic peeling program that will unravel (multiple) loops. Alleles do not need to be recoded, so real allele sizes can be used. Genotype probabilities for a chosen person can be calculated for purposes of genetic risk calculation. Later versions include one for calculations using linked markers and mutations and mosaicism, made by Martin van der Meulen. A symbolic versions will generate the formula to compute the pedigree likelihood. (entry from Genetic Analysis Software)

Proper citation: GRONLOD (RRID:SCR_009049) Copy   

•   Source: SciCrunch Registry

http://www.biodata.ee/SNPassistant.htm (30 days trial version)

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for SNP data managing, import & export from linkage format, data validation, pairwise LD calculation and visualisation, case-control and TDT tests, visual comparison of two datasets, relationships testing. Suitable for large projects.

Proper citation: SNP ASSISTANT (RRID:SCR_009048) Copy   

•   Source: SciCrunch Registry

http://genapha.icapture.ubc.ca/PathTutorial/

Web application to investigate gene-gene interactions in genetic association studies designed to: 1. Interface your SNP data with biological information from several online bioinformatics databases. 2. Generate biologically plausible hypotheses for testing gene-gene interactions. 3. Select a subset of SNPs and conduct SNP-SNP interaction tests. 4. Store analysis results. 5. Explore analysis results through interactive plots and summary tables. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PATH (RRID:SCR_009042) Copy   

•   Source: SciCrunch Registry

http://www.uni-bonn.de/~umt70e/becker.html

Software application for haplotype association analysis of unphased genotype data. It can be used both for population data (case-control) and nuclear family data. The program is optimized for haplotype frequency estimation with the EM-algorithm for many markers. FAMHAP provides a method which searches for potential genotyping errors and several tests for haplotype-based association analysis. Particular emphasis is on Monte-Carlo simulations, which are necessary in the context of haplotype association, where asymptotic theory often fails, and in the context of multiple testing problems. (entry from Genetic Analysis Software)

Proper citation: FAMHAP (RRID:SCR_009070) Copy   

•   Source: SciCrunch Registry

http://www.simedic.com.ar/bdgen.htm

Powerful database software with improvement tools for paternity testing, database searching (like CODIS) and NRC II recommendations based formulae for investigating likelyhood ratios in putative contributors to crime evidences. Additional genetic population parameters estimations are added in this version. Only spanish version available. (entry from Genetic Analysis Software)

Proper citation: BDGEN (RRID:SCR_008811) Copy   

•   Source: SciCrunch Registry

http://www.statistics.com/software-directory/helixtree

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016.

Proper citation: HELIXTREE (RRID:SCR_009067) Copy   

•   Source: SciCrunch Registry