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http://www.imbs.uni-luebeck.de/pub/minsage/index.html

Software application to calculate the sample size of genotypes minimally required to ensure that all alleles with a specified frequency at one locus are detected with a given confidence (entry from Genetic Analysis Software)

Proper citation: MINSAGE (RRID:SCR_009293) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/stephens/software.html

Software program that implements a new statistical method for reconstructing haplotypes from population genotype data (entry from Genetic Analysis Software)

Proper citation: PHASE (RRID:SCR_009327) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,20023. Software application for identifying all Mendelian inconsistencies in pedigree data. (entry from Genetic Analysis Software)

Proper citation: PEDCHECK (RRID:SCR_009322) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/abecasis/Pedstats/

Software application for error checking and data summary of large or small data sets in QTDT, LINKAGE or MENDEL format. Checks for basic formatting errors, disconnected family groups, ancestor-descendant loops and can detect all Mendelian (including X-linked) inheritance errors in any pedigree without loops. Produces text and graphical (PDF) summaries of the family structure, trait and marker information of pedigree data and can break down summaries by sex, relative pair type or family. PEDSTATS also does Hardy-Weinberg testing using either a fast exact or asymptotic test and can summarize information in text or graphical PDF format. Additional features include a number of options for filtering data prior to summary and checks for inappropriate age or covariate values. Lastly, PEDSTATS can identify and trim uninformative individuals from a pedigree and rewrite the reorganized data to a new pedigree file. (entry from Genetic Analysis Software)

Proper citation: PEDSTATS (RRID:SCR_009323) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ust.hk/MegaSNPHunter.html

Software application that takes case-control genotype data as input and produces a ranked list of multi-SNP interactions. In particular, the whole genome is first partitioned into multiple short subgenomes and a boosting tree classifier is built for each subgenomes based on multi-SNP interactions and then used to measure the importance of SNPs. The method keeps relatively more important SNPs from all subgenomes and let them compete with each other in the same way at the next level. The competition terminates when the number of selected SNPs is less than the size of a subgenome. (entry from Genetic Analysis Software)

Proper citation: MEGASNPHUNTER (RRID:SCR_009287) Copy   

•   Source: SciCrunch Registry

http://carlit.toulouse.inra.fr/MCQTL/

Software package to perform QTL mapping in multi-cross designs that allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all them. Moreover, a diallel modelling of the QTL genotypic effects is allowed in multiple related families. Obviously, the analysis of a single cross is also feasible. (entry from Genetic Analysis Software)

Proper citation: MCQTL (RRID:SCR_009285) Copy   

•   Source: SciCrunch Registry

http://www-genome.wi.mit.edu/genome_software

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

Proper citation: MAPMAKER/QTL (RRID:SCR_009283) Copy   

•   Source: SciCrunch Registry

http://ib.berkeley.edu/labs/slatkin/eriq/software/mdb_web/

Software application using the mimimum description length model to delineate haplotype blocks (entry from Genetic Analysis Software)

Proper citation: MDBLOCKS (RRID:SCR_009280) Copy   

•   Source: SciCrunch Registry

http://hgc.sph.uth.tmc.edu (not available yet)

Software program for determining biological relatedness between individuals based on allele sharing at microsatellite loci (entry from Genetic Analysis Software)

Proper citation: RELTYPE (RRID:SCR_009359) Copy   

•   Source: SciCrunch Registry

http://www.biostat.jhsph.edu/~kbroman/software/

Software program for verifying the relationships between all pairs of individuals in a linkage study, by use of (autosomal) genome scan data, with allowance for the presence of genotyping errors. (entry from Genetic Analysis Software)

Proper citation: RELCHECK (RRID:SCR_009357) Copy   

•   Source: SciCrunch Registry

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

Software program that infers the relationships of pairs of individuals based on genetic marker data, either within families or across an entire sample. (entry from Genetic Analysis Software)

Proper citation: RELPAIR (RRID:SCR_009358) Copy   

•   Source: SciCrunch Registry

http://www.uni-bonn.de/~umt70e/soft.htm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application using a family-based association method that allows testing for linkage in the presence of linkage disequilibrium between an autosomal marker and a disease even if there is only incomplete parental-marker information. Recently, Horvath et al. (2000) described a similar procedure (XRC-TDT) for X-linked markers. The distribution contains SAS macros that calculate the RC-TDT and XRC-TDT test statistics, as well as their respective exact P values. (entry from Genetic Analysis Software)

Proper citation: RC-TDT (RRID:SCR_009353) Copy   

•   Source: SciCrunch Registry

http://qtl.cap.ed.ac.uk/

A web-based user-friendly package to map Quantitative Trait Loci in outbred populations. Population structures catered for are line crosses, halfsib families, nuclear families and sibpairs. Permutation tests to determine empirical significance levels and bootstrapping to estimate empirical confidence intervals of QTL locations are optional. Fixed effects/covariates can be fitted and models may include single or multiple QTL. Results are presented in tabular and graphical format. (entry from Genetic Analysis Software)

Proper citation: QTL EXPRESS (RRID:SCR_009350) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software package designed to make as many as possible of the new statistics (e.g. score statistics) widely available. The software consists of a MEGA2-like interface for data analysis preparation and a library of R routines that computes linkage statistics. QTL-ALL reads in input data, creates re-formatted output data files, calls external IBD-generation software such as MERLIN or SIMWALK2, then computes statistics using our R library, and finally produces tables and plots of statistics and p-values. This entire sequence is highly automated, requiring minimal user-intervention. The initial release of the software computes a number of newer QTL-mapping statistics, including several score statistic variants, and can handle nuclear family data, including specialty designs such as discordant and concordant (affected) pairs. (entry from Genetic Analysis Software)

Proper citation: QTL-ALL (RRID:SCR_009348) Copy   

•   Source: SciCrunch Registry

http://statgen.ncsu.edu/qtlcart/cartographer.html

Software program to map quantitative traits sing a map of molecular markers. (entry from Genetic Analysis Software)

Proper citation: QTL Cartographer (RRID:SCR_009349) Copy   

•   Source: SciCrunch Registry

http://www.helsinki.fi/~tsjuntun/pseudomarker/

A linkage analysis software for joint linkage and/or linkage disequilibrium analysis. PSEUDOMARKER can analyze different data structures jointly such as cases-controls, trios, sib-pairs, sib-ships, and extended families. (entry from Genetic Analysis Software)

Proper citation: PSEUDOMARKER (RRID:SCR_009345) Copy   

•   Source: SciCrunch Registry

http://www.urmc.rochester.edu/smd/biostat/Projects/Help/PC/Software_Listings.htm

Software application for partition of single generation into sibling groups (entry from Genetic Analysis Software)

Proper citation: PRT (RRID:SCR_009340) Copy   

•   Source: SciCrunch Registry

http://acgt.cs.tau.ac.il/psat/

Software application (entry from Genetic Analysis Software)

Proper citation: PSAT (RRID:SCR_009341) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/~spencer/SelSim/

Software program which can simulate population genetic data in which a single site has experienced natural selection. When designing methods which provide the necessary power to detect regions of the genome which have experience historical selective pressures it is important to consider which patterns of genetic diversity are indicative of particular forms of natural selection. (entry from Genetic Analysis Software)

Proper citation: SELSIM (RRID:SCR_009378) Copy   

•   Source: SciCrunch Registry

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

Software environment for constructing linkage maps in outcrossing plant species, using full-sib families derived from two outbreed (non-inbreeding) parent plants. (entry from Genetic Analysis Software)

Proper citation: R/ONEMAP (RRID:SCR_009371) Copy   

•   Source: SciCrunch Registry