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http://www-math.u-strasbg.fr/genpred/spip.php?article3

R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Cascade (RRID:SCR_005861) Copy   

•   Source: SciCrunch Registry

http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape''''s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

Proper citation: BiNGO: A Biological Networks Gene Ontology tool (RRID:SCR_005736) Copy   

•   Source: SciCrunch Registry

http://snpeff.sourceforge.net/

Genetic variant annotation and effect prediction software toolbox that annotates and predicts effects of variants on genes (such as amino acid changes). By using standards, such as VCF, SnpEff makes it easy to integrate with other programs.

Proper citation: SnpEff (RRID:SCR_005191) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/rbsurv.html

Software package that selects genes associated with survival.

Proper citation: rbsurv (RRID:SCR_001175) Copy   

•   Source: SciCrunch Registry

http://www.litinspector.org/

A literature search tool providing gene and signal transduction pathway mining within NCBI''''s PubMed database. Its sophisticated gene recognition and intuitive color coding increase the readability of abstracts and lets you analyze signal transduction pathways, diseases and tissue associations in a snap. Note: LitInspector has become part of the Literature & Pathways module of the Genomatix Software Suite.

Proper citation: LitInspector (RRID:SCR_011870) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/bars.htm

Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BARS (RRID:SCR_009123) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/hclust/hclust.htm

Software application that is a simple clustering method that can be used to rapidly identify a set of tag SNP's based upon genotype data (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: HCLUST (RRID:SCR_009154) Copy   

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http://sourceforge.net/projects/phenofam/

A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms.

Proper citation: PhenoFam (RRID:SCR_000640) Copy   

•   Source: SciCrunch Registry

http://faculty.washington.edu/browning/floss/floss.htm

Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software)

Proper citation: FLOSS (RRID:SCR_000836) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/dindel

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems).

Proper citation: DINDEL (RRID:SCR_001827) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/pedigraph/

A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles

Proper citation: PEDIGRAPH (RRID:SCR_001938) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/igblast/

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine.

Proper citation: IgBLAST (RRID:SCR_002873) Copy   

•   Source: SciCrunch Registry

http://sybil.sourceforge.net/

A web-based software package for comparative genomics.

Proper citation: Sybil (RRID:SCR_005593) Copy   

•   Source: SciCrunch Registry

http://www.gramene.org

Curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species to facilitate the study of cross-species comparisons using information generated from projects supported by public funds. It currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. The web-based displays for phenotypes include the Genes and Quantitative Trait Loci (QTL) modules. Sequence based relationships are displayed in the Genomes module using the genome browser adapted from Ensembl, in the Maps module using the comparative map viewer (CMap) from GMOD, and in the Proteins module displays. BLAST is used to search for similar sequences. Literature supporting all the above data is organized in the Literature database. In addition, Gramene now hosts a variety of web services including a Distributed Annotation Server (DAS), BLAST and a public MySQL database. Twice a year, Gramene releases a major build of the database and makes interim releases to correct errors or to make important updates to software and/or data. Additionally you can access Gramene through an FTP site.

Proper citation: Gramene (RRID:SCR_002829) Copy   

•   Source: SciCrunch Registry

https://genenames.org

Only worldwide authority that provides standardized nomenclature, i.e. gene names and symbols (short form abbreviations), for all known human genes, and stores all approved symbols in the HGNC database. Approved human gene nomenclature. Database of gene symbols and names. Manually curated genes into groups based on shared characteristics such as homology, function or phenotype. Data for protein-coding genes, pseudogenes and non-coding RNAs.

Proper citation: HGNC (RRID:SCR_002827) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/gsea/

Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.

Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) 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.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://archive.broadinstitute.org/mpg/sweep/

Software application that allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype test to look for alleles of high frequency with long-range linkage disequilibrium, which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers. SWEEP takes phased genotype data as input, detects all haplotype blocks in that data, and then determines the frequency and long-range LD for each allele in each block. (entry from Genetic Analysis Software)

Proper citation: SWEEP (RRID:SCR_009418) Copy   

•   Source: SciCrunch Registry

http://www.jurgott.org/linkage/sumstat.html

Software application that assess the joint disease association of multiple unlinked SNPs via sums of SNP specific test statistics. Genome-wide significance levels are obtained by per mutation analysis. (entry from Genetic Analysis Software)

Proper citation: SUMSTAT (RRID:SCR_009416) Copy   

•   Source: SciCrunch Registry