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http://bc02.iis.sinica.edu.tw/gobu/manual/index.html

Gene Ontology Browsing Utility (GOBU) (GOBU) is a Java-based software program for integrating biological annotation catalogs under an extendable software architecture. Users may interact with the Gene Ontology and user-defined hierarchy data of genes, and then use its plugins to (and not limited to) (1) browse the GO hierarchy with user defined data, (2) browse GO-oriented expression levels in the user data, (3) compute GO enrichment, and/or (4) customize data reporting. A set of classes and utility functions has been established so that a customized program can be made as a plugin or a command-line tool that programmically manipulate the Gene Ontology and specified user data. See the source code repository for examples. Reference Lin WD, Chen YC, Ho JM, Hsiao CD. GOBU: Toward an Integration Interface for Biological Objects. Journal of Information Science and Engineering. 2006 22(1):19-29. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: Gene Ontology Browsing Utility (GOBU) (RRID:SCR_005662) Copy   

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http://www.sgn.cornell.edu/bulk/input.pl?modeunigene

Allows users to download Unigene or BAC information using a list of identifiers or complete datasets with FTP., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Sol Genomics Network - Bulk download (RRID:SCR_007161) Copy   

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http://linux1.softberry.com/spldb/SpliceDB.html

Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs.

Proper citation: SpliceDB (RRID:SCR_006262) Copy   

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http://aws.amazon.com/1000genomes/

A dataset containing the full genomic sequence of 1,700 individuals, freely available for research use. The 1000 Genomes Project is an international research effort coordinated by a consortium of 75 companies and organizations to establish the most detailed catalogue of human genetic variation. The project has grown to 200 terabytes of genomic data including DNA sequenced from more than 1,700 individuals that researchers can now access on AWS for use in disease research free of charge. The dataset containing the full genomic sequence of 1,700 individuals is now available to all via Amazon S3. The data can be found at: http://s3.amazonaws.com/1000genomes The 1000 Genomes Project aims to include the genomes of more than 2,662 individuals from 26 populations around the world, and the NIH will continue to add the remaining genome samples to the data collection this year. Public Data Sets on AWS provide a centralized repository of public data hosted on Amazon Simple Storage Service (Amazon S3). The data can be seamlessly accessed from AWS services such Amazon Elastic Compute Cloud (Amazon EC2) and Amazon Elastic MapReduce (Amazon EMR), which provide organizations with the highly scalable compute resources needed to take advantage of these large data collections. AWS is storing the public data sets at no charge to the community. Researchers pay only for the additional AWS resources they need for further processing or analysis of the data. All 200 TB of the latest 1000 Genomes Project data is available in a publicly available Amazon S3 bucket. You can access the data via simple HTTP requests, or take advantage of the AWS SDKs in languages such as Ruby, Java, Python, .NET and PHP. Researchers can use the Amazon EC2 utility computing service to dive into this data without the usual capital investment required to work with data at this scale. AWS also provides a number of orchestration and automation services to help teams make their research available to others to remix and reuse. Making the data available via a bucket in Amazon S3 also means that customers can crunch the information using Hadoop via Amazon Elastic MapReduce, and take advantage of the growing collection of tools for running bioinformatics job flows, such as CloudBurst and Crossbow.

Proper citation: 1000 Genomes Project and AWS (RRID:SCR_008801) Copy   

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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   

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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   

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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   

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http://ftp://statgen.ncsu.edu/pub/zaykin/

Software application performing a shuffling version of the exact conditional tests for different combinations of allelic and genotypic disequilibrium on haploid and diploid data, or their combination. (entry from Genetic Analysis Software)

Proper citation: MLD (RRID:SCR_009298) Copy   

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http://ftp://ftp.biomath.jussieu.fr/pub/mlbgh (not available)

Software application that is an extension of the GENEHUNTER program to perform sib-pair and sib-ship linkage analysis using the Maximum Likelihood Binomial (MLB) method. (entry from Genetic Analysis Software)

Proper citation: MLBGH (RRID:SCR_009297) Copy   

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http://www.uni-kiel.de/medinfo/mitarbeiter/krawczak/download/index.html

Software application (entry from Genetic Analysis Software)

Proper citation: MKGST (RRID:SCR_009295) Copy   

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

Software application (entry from Genetic Analysis Software)

Proper citation: PLABSIM (RRID:SCR_009328) Copy   

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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   

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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   

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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   

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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