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http://www.medgen.de/index.html

Powerful pedigree drawing program with two drawing modes: Input mode for fast and automatic drawing; edit mode for text annotations, legends, special symbols. Both input and edit mode provide auto numbering, auto resizing of symbols and fonts, and zooming. PED 4.2a complies with the Recommendations for standardized human pedigree nomenclature. Apart from fully sizeable printed output, pedigrees can be exported as metafiles to virtually any Windows word processor or drawing program. (entry from Genetic Analysis Software)

Proper citation: PED (RRID:SCR_009320) Copy   

•   Source: SciCrunch Registry

http://www.genetics.ucla.edu/software/

Software application for genetic analysis of human pedigree data under models involving a small number of loci. MENDEL is useful for segregation analysis, linkage calculations, genetic counseling, allele frequency estimation, and related kinds of problems. (entry from Genetic Analysis Software)

Proper citation: MENDEL (RRID:SCR_009288) Copy   

•   Source: SciCrunch Registry

http://pedagree.free.fr/

Software program for detecting autosomal marker Mendelian incompatibilities in pedigree data (entry from Genetic Analysis Software)

Proper citation: PEDAGREE (RRID:SCR_009321) Copy   

•   Source: SciCrunch Registry

http://ftp://linkage.rockefeller.edu/software/relative

Software application for relationship estimation, in particular between putative sibs when parents are untyped (entry from Genetic Analysis Software)

Proper citation: RELATIVE (RRID:SCR_009355) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/RelativeFinder

Software program for checking relationships between pairs of individuals. There are many excellent programs that carry out similar tasks. Some of the unique features in relativeFinder are the batch mode options, that allow large jobs to be divided into many smaller jobs (suitable for deployment on a compute cluster environment), and the flexibility of the underlying Merlin engine, which allows relative finder to handle large pedigrees and consider a variety of alternate relationships -- including potential relationships specified by the user on the fly. (entry from Genetic Analysis Software)

Proper citation: RELATIVEFINDER (RRID:SCR_009356) Copy   

•   Source: SciCrunch Registry

http://bioinfo.ebc.ee/download/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Tag SNP selection tool according to r2-bins method that is specifically designed for full genome scale deterministic tagging.

Proper citation: REAPER (RRID:SCR_009354) Copy   

•   Source: SciCrunch Registry

http://pig.ag.uq.edu.au/qu-gene/ (not available)

Software package for quantitative analysis of genetic models (entry from Genetic Analysis Software)

Proper citation: QU-GENE (RRID:SCR_009351) Copy   

•   Source: SciCrunch Registry

http://www.riscalw.uni-hd.de

Windows program for risk calculation in families with Duchenne muscular dystrophy. It is based on an extended genetic model which includes germline mosaicism and different new mutation rates depending on sex and mutation type. Arbitrary family structures and additional diagnostic information like genotypes from intragenetic and flancing genetic markers of the dystrophin gene, creatin kinase values and female deletion test results can be taken into account. (entry from Genetic Analysis Software)

Proper citation: RISCALW (RRID:SCR_009352) Copy   

•   Source: SciCrunch Registry

http://www.jax.org/staff/churchill/labsite/software/pseudomarker/index.html

A set of programs written in MATLAB for the analysis of QTL data from inbred line crosses. (entry from Genetic Analysis Software)

Proper citation: PSEUDOMARKER.M (RRID:SCR_009346) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/pseudo/download

Software application that estimates genomewide empirical p-values for Kong and Cox tests of linkage using the replicate pool method, which for many data sets, improves upon the computational efficiency of conventional gene-dropping methods by several orders of magnitude. This allows Pseudo to handle data sets with large families and makes it particularly applicable to those situations where p-value estimation by standard methods is computationally prohibitive. Pseudo also estimates variance for reported p-values, produces graphical and text summaries of results, and is able to assess significance of multiple correlated outcomes. Pseudo is designed to work with the Merlin package and includes utilities for generating input files from standard Merlin output. (entry from Genetic Analysis Software)

Proper citation: PSEUDO (RRID:SCR_009344) Copy   

•   Source: SciCrunch Registry

http://support.sas.com/documentation/onlinedoc/genetics/

Software application for summarizing marker properties (allele & genotype frequencies, tests for Hardy-Weinberg equilibrium, measures of marker informativeness), examining marker-marker relationships (tests and measures of linkage disequilibrium, and haplotype frequency estimation), and exploring marker-trait associations using case-control or family-based tests (entry from Genetic Analysis Software)

Proper citation: SAS/GENETICS (RRID:SCR_009343) Copy   

•   Source: SciCrunch Registry

http://www.maths.lancs.ac.uk/~fearnhea/Hotspot/

Software program that analyzes sequence data. It obtains an approximation to the likelihood of a summary of the data (as such it can be thought of as a marginal likelihood approach). It does not use all the information in the data, but computationally it can be substantially more efficient than the full-likelihood methods (and hence able to analyze larger data sets). (entry from Genetic Analysis Software)

Proper citation: SEQUENCE LD/SEQUENCE LDHOT (RRID:SCR_009379) Copy   

•   Source: SciCrunch Registry

https://www.dkfz.de/en/epidemiologie-krebserkrankungen/software/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software program for fast calculation of empirical and adjusted p-values for correlated and uncorrelated hypotheses in multiple testing experiments. It is based on the Free Step-Down Resampling Method for controlling the Family Wise Error Rate, originally proposed by Westfall and Young (1993), and implements a variation of the efficient algorithm of Ge et al. (2003), in which the originally necessary re-sampling effort was reduced considerably and the method made computationally more feasible. The program is independent of the underlying test statistic and works with provided observed and permutation test statistics. (entry from Genetic Analysis Software)

Proper citation: SDMINP (RRID:SCR_009377) Copy   

•   Source: SciCrunch Registry

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

An R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files. (entry from Genetic Analysis Software)

Proper citation: R/SNP.PLOTTER (RRID:SCR_009376) Copy   

•   Source: SciCrunch Registry

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

An R package that uses an individual-based approach to simulate distributions of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization). These distributions can be used to test new or existing population-genetics summary statistics or develop null distributions under various demographies. (entry from Genetic Analysis Software)

Proper citation: R/METASIM (RRID:SCR_009370) Copy   

•   Source: SciCrunch Registry

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

http://www.rosettabio.com/products/syllego/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 2, 2014. A genetic data management and analysis system designed to advance your whole genome association, linkage, and eQTL studies, providing you with an easy-to-use project workspace so that you can organize, analyze, and share your genotype and phenotype data along with your analysis results. With the Syllego system, generating high quality analysis data and meaningful results becomes simple. The Syllego system automates all tedious data management and data formatting tasks so that you can streamline your genetic analysis workflows using your analysis methods of choice. Managing all your genetic data and reference information is straightforward. The Syllego system converts public and private genotype data sets and reference annotations, such as dbSNP and HapMap, as well as individual (sample) information into a single, consistent repository for fast, convenient access. (entry from Genetic Analysis Software)

Proper citation: ROSATTA SYLLEGO SYSTEM (RRID:SCR_009363) Copy   

•   Source: SciCrunch Registry

http://research.nhgri.nih.gov/ROMPrev/

Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software)

Proper citation: ROMPREV (RRID:SCR_009361) Copy   

•   Source: SciCrunch Registry

http://www.pass-software.com/Producten/PASSPedigree.aspx (in Dutch)

Software application to draw the most complex family trees in a matter of minutes instead of hours of work. The basis of this is an algorithm for automatically builing a family tree. Of course, manual adjustments in the family tree can be made for your specific requirements. PASS Pedigree meets all international conventions concerning the drawing of pedigrees. A converter can convert historical Cyrillic pedigrees automatically to PASS Pedigree. Unlike before, all your family trees are stored in one single database. PASS Pedigree can intelligently connect to many genetic centers (e.g. three genetic centers in the Netherlands) with the existing patient information, via the lab system HELIX based on HL7 techniques. (entry from Genetic Analysis Software)

Proper citation: PASS PEDIGREE (RRID:SCR_009315) Copy   

•   Source: SciCrunch Registry

http://ibi.imim.es/osirisform.html

Software tool for the retrieval of articles from MEDLINE related to the sequence variants reported for a human gene. The variations considered are single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (indel), microsatellite, and named variations (e.g. Alu sequences). (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OSIRIS (RRID:SCR_009313) Copy   

•   Source: SciCrunch Registry