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http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer/

A webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region.

Proper citation: CandiSNPer (RRID:SCR_005173) Copy   

•   Source: SciCrunch Registry

http://sadiframework.org/

Framework for discovery of, and interoperability between, distributed data and analytical resources. It combines GET/POST-based Web Services with standards from the W3C Semantic Web initiative. The objective is to make it easy for data and analytical tool providers to make their resources available on the Semantic Web with minimal disruption to their usual practices. It simply defines an open set of best-practices and conventions, within the spectrum of existing standards, that allow for a high degree of semantic discoverability and interoperability between participating services.

Proper citation: Semantic Automated Discovery and Integration (RRID:SCR_004130) Copy   

•   Source: SciCrunch Registry

http://www.uniprot.org/uniparc/

Database that contains publicly available protein sequences with stable and unique identifiers (UPI) which are never removed, changed or reassigned. UniParc tracks sequence changes in the source databases and archives the history of all changes. Information other than protein sequence must be retrieved from the UniParc source databases using the database cross-references.

Proper citation: UniParc (RRID:SCR_005818) Copy   

•   Source: SciCrunch Registry

http://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hox-pro00.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 11th,2023. The database HOX Pro contains information about organization, functions and evolution of gene ensembles, key roles in which play homeobox-genes. It is aimed at: 1. analysis and classification of regulatory and coding regions in diverse homeobox and related genes; 2. describing mutations and knock-outs of hox-genes, as well as hereditary diseases related to these genes; 3. graphical representation, comparisons and classification of hox-genes expression patterns and profiles (sea urchin blastula, Drosophila blastoderm and imaginal discs, vertebrate limbs, mammalian brain, human EC cells); 4. comparative analysis of organization of hox-based genetic networks the nematode Caenorhabditis elegans the sea urchins Strongylocentrotus purpuratus and other echinids, the fruit flies Drosophila melanogaster and D.virilis, the vertebrates chicken and mouse; 5. analysis of phylogeny and evolution of homeobox genes and clusters.

Proper citation: Homeobox Genes DataBase (RRID:SCR_007723) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/pooling/poolscore.htm

Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software)

Proper citation: POOLSCORE (RRID:SCR_007514) Copy   

•   Source: SciCrunch Registry

http://www.mybiosoftware.com/genecounting-2-2-gene-counting-haplotype-analysis.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application for gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data.

Proper citation: GENECOUNTING (RRID:SCR_009189) Copy   

•   Source: SciCrunch Registry

http://episun7.med.utah.edu/~alun/gchap/index.html

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals. By excluding haplotypes with zero MLE at an early stage, this implementation uses many orders of magnitude less space and time than naive implementations. A second program, ApproxGCHap, is provided to give alternate estimates for data sets with large numbers of loci or large amounts of missing genotypes.

Proper citation: GCHAP (RRID:SCR_009186) Copy   

•   Source: SciCrunch Registry

http://www.epicentersoftware.com/products.php

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 21, 2016. Software package for the management and analysis of pedigree data. it offers: 1. Powerful database management tools, specifically designed for family data; 2. Automatic pedigree drawing; 3. Segregation and linkage analysis, based on traditional maximum likelihood methods and newer, more powerful, Monte Carlo methods that can model both genetic and environmental factors. (entry from Genetic Analysis Software)

Proper citation: GAP (RRID:SCR_009183) Copy   

•   Source: SciCrunch Registry

http://evolution.genetics.washington.edu/lamarc/lamarc_prog.html

Software application that estimates effective population sizes, exponential population growth rates, and past migration rates between two or n populations, and simultaneously estimates the per-nucleotide recombination rate. Currently Lamarc can use DNA or RNA sequence data, SNP data, and microsatellite data. (entry from Genetic Analysis Software)

Proper citation: LAMARC (RRID:SCR_009252) Copy   

•   Source: SciCrunch Registry

http://people.virginia.edu/~wc9c/KING/

Software toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) for applications such as family relationship inference and population structure identification (entry from Genetic Analysis Software)

Proper citation: KING (RRID:SCR_009251) Copy   

•   Source: SciCrunch Registry

http://www.genepi.org.au/jlin

Software application designed for customizable, intuitive visualisation of LD analysis across all common computing platforms. Customisation allows the researcher to choose particular visualisation, statistical measures and measurement ranges. JLIN also allows the researcher to export images of the LD visualisation in several common document formats. As there appears to be no single best measure of LD under all possible circumstances, JLIN allows the researcher to visually compare and contrast the results of a range of statistical measures on the input data set(s). These measures include the commonly used D'' and R2 statistics and empirical p-values. New additions include calculation of HWE, a completely revamped interface, and a numer of minor bug fixes. We have added a display measure to show marker distances visually, embedded fonts to improve image clarity and additional LD measures including d,OR,Pexcess and Q. (entry from Genetic Analysis Software)

Proper citation: JLIN (RRID:SCR_009247) Copy   

•   Source: SciCrunch Registry

http://www.joinmap.nl/

Software application for construction of genetic linkage maps for several types of mapping populations: BC1, F2, RILs, (doubled) haploids, outbreeders full-sib family. Can combine (''join'') data derived from several sources into an integrated map. Further: linkage group determination, automatic phase determination for outbreeders full-sib family, several diagnostics, and map charts. Everything available in an intuitive MS-Windows user interface. (entry from Genetic Analysis Software)

Proper citation: JOINMAP (RRID:SCR_009248) Copy   

•   Source: SciCrunch Registry

https://mathgen.stats.ox.ac.uk/impute/impute.html

Software application for estimating (imputing) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST. (entry from Genetic Analysis Software)

Proper citation: IMPUTE (RRID:SCR_009245) Copy   

•   Source: SciCrunch Registry

http://chgr.mc.vanderbilt.edu/ritchielab/method.php?method=mdrpdt

Software application (entry from Genetic Analysis Software)

Proper citation: MDR-PDT (RRID:SCR_009243) Copy   

•   Source: SciCrunch Registry

http://intersnp.meb.uni-bonn.de/

Software application for genome-wide interaction analysis (GWIA) of case-control SNP data. SNPs are selected for joint analysis using a priori information. Sources of information to define meaningful strategies can be statistical evidence (single marker association at a moderate level, computed from the own data) and genetic/biologic relevance (genomic location, function class or pathway information). (entry from Genetic Analysis Software)

Proper citation: INTERSNP (RRID:SCR_009244) Copy   

•   Source: SciCrunch Registry

http://www.chgb.org.cn/htSNPer/htSNPer.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 4, 2023.Java program for characterizing the haplotype block structure and selecting haplotype tagging SNP (entry from Genetic Analysis Software)

Proper citation: HTSNPER (RRID:SCR_009242) Copy   

•   Source: SciCrunch Registry

http://www.math.mtu.edu/~shuzhang/software.html

Software application for testing association using tightly linked markers in nuclear pedigrees (entry from Genetic Analysis Software)

Proper citation: HS-TDT (RRID:SCR_009240) Copy   

•   Source: SciCrunch Registry

http://www.biomath.medsch.ucla.edu/faculty/klange/software.html

THIS RESOURCE IS NO LOGER IN SERVICE. Documented on May 16,2023. A simple dBASE III program for the management of pedigree and locus data. It permits easy extraction of genetic data for use with MENDEL and FISHER. (entry from Genetic Analysis Software)

Proper citation: DGENE (RRID:SCR_009158) Copy   

•   Source: SciCrunch Registry

http://www.infobiogen.fr/services/CoPE

Software application that includes a Java program for drawing pedigrees and a standardized system for pedigree storage. Unlike other existing pedigree programs, this software is particularly intended for epidemiologists in the sense that it allows customized automatic drawing of large numbers of pedigrees and remote and distributed consultation of pedigrees. (entry from Genetic Analysis Software)

Proper citation: COPE (RRID:SCR_009153) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that is an implementation of a genome-based scan statistic that detects genomic regions.

Proper citation: CHROMOSCAN (RRID:SCR_009151) Copy   

•   Source: SciCrunch Registry