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http://c2s2.yale.edu/software/lot/

Software application (entry from Genetic Analysis Software)

Proper citation: LOT (RRID:SCR_009261) Copy   

•   Source: SciCrunch Registry

http://www.uoguelph.ca/~rdanzman/software/PROBMAX/

Software application for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny (entry from Genetic Analysis Software)

Proper citation: PROBMAX (RRID:SCR_009337) Copy   

•   Source: SciCrunch Registry

http://www.statgen.ucr.edu/software.html

Software application that is a user defined SAS procedure for mapping quantitative trait loci (QTL). Since this procedure is not a built-in SAS procedure, users need to obtain a copy of the executable file of PROC QTL and install the software in their personal computers before PROC QTL can be executed. Of course, users need a regular SAS license prior to the installation of PROC QTL. Once PROC QTL is installed, it can be called just like any other SAS procedures. Users will not notice the differences between this customized procedure and other built-in SAS procedures. (entry from Genetic Analysis Software)

Proper citation: PROC QTL (RRID:SCR_009338) Copy   

•   Source: SciCrunch Registry

http://phg.mc.vanderbilt.edu/content/powertrim

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11,2023. Software application that automate the decision to remove objects from a pedigree with a minimum loss information (entry from Genetic Analysis Software)

Proper citation: POWERTRIM (RRID:SCR_009333) Copy   

•   Source: SciCrunch Registry

http://www.uni-hohenheim.de/~frisch/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: PLABSIM (RRID:SCR_009328) Copy   

•   Source: SciCrunch Registry

http://www.people.fas.harvard.edu/~junliu/plem/

Software application (entry from Genetic Analysis Software)

Proper citation: PL-EM (RRID:SCR_009329) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/peer/

Software collection of Bayesian approaches to infer hidden determinants and their effects from gene expression profiles using factor analysis methods. Applications of PEER have * detected batch effects and experimental confounders * increased the number of expression QTL findings by threefold * allowed inference of intermediate cellular traits, such as transcription factor or pathway activations This project offers an efficient and versatile C++ implementation of the underlying algorithms with user-friendly interfaces to R and python.

Proper citation: PEER (RRID:SCR_009326) Copy   

•   Source: SciCrunch Registry

http://www.sfbr.org/sfbr/public/software/pedsys/pedsys.html

Full-scale database system developed as a specialized tool for management of genetic, pedigree and demographic data. (entry from Genetic Analysis Software)

Proper citation: PEDSYS (RRID:SCR_009324) Copy   

•   Source: SciCrunch Registry

http://www.pedvizapi.org/

A Java Api for the visual analysis of large and complex pedigrees that provides all the necessary functionality for the interactive exploration of extended genealogies. Available packages are mostly focused on a static representation or cannot be added to an existing application; the goal of this open-source library is to provide an application program interface that enables the efficient construction of visual analytic applications for the analysis of family based data. (entry from Genetic Analysis Software)

Proper citation: PEDVIZAPI (RRID:SCR_009325) Copy   

•   Source: SciCrunch Registry

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://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://archive.broadinstitute.org/mpg/tagger/

Software application (entry from Genetic Analysis Software)

Proper citation: TAGGER (RRID:SCR_009419) Copy   

•   Source: SciCrunch Registry