Tools   Select Another Resource Report Type

http://www.adfg.alaska.gov/index.cfm?adfg=fishinggeneconservationlab.software

Software application that estimates the relative contributions of discrete populations to a mixture sample, solving what is commonly referred to in fisheries as the mixed stock analysis or genetic stock identification problem. (entry from Genetic Analysis Software)

Proper citation: SPAM (RRID:SCR_009407) Copy   

•   Source: SciCrunch Registry
  

https://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html

Software program for the analysis of single SNP association in genome-wide studies. The tests implemented can cater for binary (case-control) and quantitative phenotypes, can condition upon an arbitrary set of covariates and properly account for the uncertainty in genotypes. The program is designed to work seamlessly with the output of both the genotype calling program CHIAMO, the genotype imputation program IMPUTE and the program GTOOL. This program was used in the analysis of the 7 genome-wide association studies carried out by the Wellcome Trust Case-Control Consortium (WTCCC). (entry from Genetic Analysis Software)

Proper citation: SNPTEST (RRID:SCR_009406) Copy   

•   Source: SciCrunch Registry
  

http://www.icr.ac.uk/cancgen/molgen/MolPopGen_Bioinformatics.htm

Software application for multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. SNPLINK requires these other programs installed on the system: MERLIN (used for nonparametric analysis), ALLEGRO (used for parametric analysis), R and PERL, all are freely available. (entry from Genetic Analysis Software)

Proper citation: SNPLINK (RRID:SCR_009403) Copy   

•   Source: SciCrunch Registry
  

http://orclinux.creighton.edu/snpp/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. A dynamic general database management system to manage high-throughput SNP genotyping data. It provides several functions, including data importing with comparison, Mendelian inheritance check within pedigrees, data compiling and exporting. Furthermore, SNPP may generate files for repeat genotyping and transform them into files that can be executed by a liquid handling system.

Proper citation: SNPP (RRID:SCR_009404) Copy   

•   Source: SciCrunch Registry
  

http://capella.uni-kiel.de/snap/snap.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software program can be used to generate SNP haplotype sequence data of unrelated individuals and nuclear families with a fixed or random number of children.

Proper citation: SNAP 3 (RRID:SCR_009400) Copy   

•   Source: SciCrunch Registry
  

http://www.chg.duke.edu/software/pdt.html

Software analysis program to evaluate evidence of linkage disequilibrium (LD) in general pedigree data. All family data may be used without nullifying the validity of the association test, even when there is more than one affected in a family. The PDT program performs both allele-specific and genotype-specific LD analysis of individual markers. Version 5.1 adds the ability to perform genotype-specific analysis over marker sets. (entry from Genetic Analysis Software)

Proper citation: PDT (RRID:SCR_009319) Copy   

•   Source: SciCrunch Registry
  

http://www.ibms.sinica.edu.tw/~csjfann/first%20flow/programlist.htm

Software tool for analyses of pooled DNA data (entry from Genetic Analysis Software)

Proper citation: PDA (RRID:SCR_009317) Copy   

•   Source: SciCrunch Registry
  

http://cougar.fhcrc.org/software.php

Software application that is a Windows-based system designed for pedigree data management, providing a graphical interface for pedigree construction and output. (entry from Genetic Analysis Software)

Proper citation: PDPSYS (RRID:SCR_009318) Copy   

•   Source: SciCrunch Registry
  

http://linkage.rockefeller.edu/pawe/

Software application for power and sample size calculations for genetic case-control association studies allowing for errors (entry from Genetic Analysis Software)

Proper citation: PAWE (RRID:SCR_009316) Copy   

•   Source: SciCrunch Registry
  

http://mlemire.freeshell.org/software.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software program that splits extended pedigrees into nuclear families, with the option of recoding all sibs as half-sibs with distinct mothers of fathers. (entry from Genetic Analysis Software)

Proper citation: NUCULAR (RRID:SCR_009311) Copy   

•   Source: SciCrunch Registry
  

http://magnet.c2b2.columbia.edu/mutagenesys/

Software application that uses genome-wide genotype data to estimate disease susceptibility. Our system integrates three data sources: HapMap, whole-genome marker correlation data, and OMIM database. It accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses even if the original set of typed SNPs is incomplete. (entry from Genetic Analysis Software)

Proper citation: MUTAGENESYS (RRID:SCR_009309) Copy   

•   Source: SciCrunch Registry
  

http://www.rni.helsinki.fi/~mjs/

Bayesian QTL mapping software for analysing backcross and F2 data from designed crossing experiments of outbred lines (entry from Genetic Analysis Software)

Proper citation: MULTIMAPPER/OUTBRED (RRID:SCR_009306) Copy   

•   Source: SciCrunch Registry
  

http://droog.gs.washington.edu/multiPopTagSelect.html

Software program that selects a near-minimal set of tagging single-nucleotide polymorphisms (tagSNPs) that account for all observed patterns of linkage disequilibrium (LD) in multiple populations. (entry from Genetic Analysis Software)

Proper citation: MULTIPOPTAGSELECT (RRID:SCR_009307) Copy   

•   Source: SciCrunch Registry
  

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

A multipoint linkage analysis software which allows Marker-Marker LD (entry from Genetic Analysis Software)

Proper citation: MULTIDISEQ (RRID:SCR_009304) Copy   

•   Source: SciCrunch Registry
  

http://www.rni.helsinki.fi/~mjs/

Bayesian QTL mapping software for analysing backcross, double haploid, and F2 data from designed crossing experiments of inbred lines (entry from Genetic Analysis Software)

Proper citation: MULTIMAPPER (RRID:SCR_009305) Copy   

•   Source: SciCrunch Registry
  

http://www.stat.sinica.edu.tw/hsinchou/genetics/pooledDNA/mpda.htm

A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software)

Proper citation: MPDA (RRID:SCR_009303) Copy   

•   Source: SciCrunch Registry
  

http://faculty.washington.edu/browning/presto/presto.html

Software application that performs permutation testing and computes empirical distributions of order statistics for one and two stage association studies with stratified or unstratified data.

Proper citation: PRESTO: Genetic Association Analysis Software (RRID:SCR_013285) Copy   

•   Source: SciCrunch Registry
  

http://pendientedemigracion.ucm.es/info/prodanim/html/JP_Web.htm

A population genetics computer program that conducts several genetic analyses on multilocus information in a user-friendly environment. Primary functions carried out by MOLKIN are the computation of the between individuals (and populations) molecular coancestry coefficients, the Kinship distance at individual and population levels. Additionally, users can compute with MOLKIN a set of among populations, genetic distances and F statistics from multilocus information. The program will help researchers or those responsible for population management to assess genetic variability and population structure at reduced costs with respect to dataset preparation (entry from Genetic Analysis Software)

Proper citation: MOLKIN (RRID:SCR_013262) Copy   

•   Source: SciCrunch Registry
  

http://www.bios.unc.edu/~lin/hapstat/

Software interface for the statistical analysis of haplotype-disease association. HAPSTAT allows the user to estimate or test haplotype effects and haplotype-environment interactions by maximizing the (observed-data) likelihood that properly accounts for phase uncertainty and study design. The current version considers cross-sectional, case-control and cohort studies. (entry from Genetic Analysis Software)

Proper citation: HAPSTAT (RRID:SCR_013382) Copy   

•   Source: SciCrunch Registry
  

http://csg.sph.umich.edu//abecasis/QTDT/

Software application that performs linkage disequilibrium (TDT) and association analysis for quantitative traits. Includes support for the methods of Abecasis et al. (2000), Fulker et al. (1999), Monks et al. (1998), Allison (TDTQ5, 1997) and Rabinowitz (1997). Supports families of any size, with or without parental information. Includes simple variance components modelling. Interfaces with SimWalk2 for IBD estimation. (entry from Genetic Analysis Software)

Proper citation: QTDT (RRID:SCR_013391) Copy   

•   Source: SciCrunch Registry