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http://www.nslij-genetics.org/soft/mapdraw.v2.2.xls

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. Software application that draws genetic linkage maps on PC same as what MAPMAKER does on Mac. (entry from Genetic Analysis Software)

Proper citation: MAPDRAW (RRID:SCR_009276) Copy   

•   Source: SciCrunch Registry

http://www.genes.org.uk/software/midas

Software application for analysis and visualisation of interallelic disequilibrium between multiallelic markers (entry from Genetic Analysis Software)

Proper citation: MIDAS (RRID:SCR_009274) Copy   

•   Source: SciCrunch Registry

http://www.biometris.wur.nl/uk/Software/MapChart/

Software application that produces charts of genetic linkage and QTL data. The charts are composed of a sequence of vertical bars representing the linkage groups or chromosomes. On these bars the positions of loci are indicated, and next to the bars QTL intervals and QTL graphs can be shown. MapChart reads the linkage information (i.e. the locus and QTL names and their positions) from text files. Many options to adapt the charts to different purposes. Can produce graphic files (enhanced windows metafile format) which can be enhanced with other MS-Windows software. (entry from Genetic Analysis Software)

Proper citation: MAPCHART (RRID:SCR_009273) Copy   

•   Source: SciCrunch Registry

http://polymorphism.ucsd.edu/cgi-bin/PRL/mama/mama.cgi

Software application (entry from Genetic Analysis Software)

Proper citation: MAMA (RRID:SCR_009270) Copy   

•   Source: SciCrunch Registry

http://www.atgc.org/XLinkage/MadMapper/

Suite of Python scripts for quality control of genetic markers, group analysis and inference of linear order of markers on linkage groups. MadMapper_RECBIT analyses raw marker scores for recombinant inbred lines. MadMapper_RECBIT generates pairwise distance scores for all markers, clusters based on pairwise distances, identifies genetic bins, assigns new markers to known linkage groups, validates allele calls, and assigns quality classes to each marker based on several criteria and cutoff values. MadMapper_XDELTA utilizes new algorithm, Minimum Entropy Approach and Best-Fit Extension, to infer linear order of markers. MadMapper_XDELTA analyzes two-dimensional matrices of all pairwise scores and finds best map that has minimal total sum of differences between adjacent cells (map with lowest entropy). MadMapper is freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software)

Proper citation: MADMAPPER (RRID:SCR_009267) Copy   

•   Source: SciCrunch Registry

http://cogent.iop.kcl.ac.uk/MaGIC.cogx

Software program to generate targeted marker sets for genome-wide association studies.

Proper citation: Marker And Gene Interpolation and Correlation (RRID:SCR_009268) Copy   

•   Source: SciCrunch Registry

http://www.hsph.harvard.edu/faculty/alkes-price/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. A software suite designed to more powerfully leverage clinical-covariates such as age, bmi, smoking status, and gender when conducting case-control association studies. Including these covariates in standard regression models is not only suboptimal, but can in many instances reduce power. LTSOFT employs a liability threshold model approach that takes advantage of known epidemiological results to better model the covariates'' relationship to the phenotype of interest (entry from Genetic Analysis Software)

Proper citation: LTSOFT (RRID:SCR_009266) Copy   

•   Source: SciCrunch Registry

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

Software application that is part of the LINKAGE auxiliary program (entry from Genetic Analysis Software)

Proper citation: LRP (RRID:SCR_009263) Copy   

•   Source: SciCrunch Registry

http://statgen.iop.kcl.ac.uk/lpop/

Software application that detects population stratification in samples of unrelated individuals for whom a number of unlinked genotypes have been measured. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: L-POP (RRID:SCR_009262) Copy   

•   Source: SciCrunch Registry

http://www.stat.washington.edu/thompson/Genepi/Loki.shtml

Software program for analyses a quantitative trait observed on large pedigrees using Markov chain Monte Carlo multipoint linkage and segregation analysis. The trait may be determined by multiple loci. (entry from Genetic Analysis Software)

Proper citation: LOKI (RRID:SCR_009260) Copy   

•   Source: SciCrunch Registry

http://mlemire.freeshell.org/SimM.README

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Gene dropping simulation software. The program is a gzip'ed tar archive and is designed to run under UNIX/Linux operating system.

Proper citation: SIMM (RRID:SCR_000849) Copy   

•   Source: SciCrunch Registry

http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. Software application that simultaneously estimates a trait-locus position and its genetic effects for affected relative pairs (ARP) by one of two methods. Either allow a different trait-locus effect for each ARP type, or constrain the trait-locus effects according to the marginal effect of a single susceptibility locus. We include a goodness of fit statistic for the constrained model. (entry from Genetic Analysis Software)

Proper citation: ARP.GEE (RRID:SCR_013134) Copy   

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http://www.broadinstitute.org/cancer/cga/oncotator

A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Genomic Annotations, Protein Annotations, and Cancer Annotations are aggregated from many resources. A standalone version of Oncotator is being developed.

Proper citation: Oncotator (RRID:SCR_005183) Copy   

•   Source: SciCrunch Registry

http://wavi.bioinfo.cnio.es/

A versatile web-server application for the analysis and visualization of array-CGH data.

Proper citation: waviCGH (RRID:SCR_006662) Copy   

•   Source: SciCrunch Registry

http://probeexplorer.cicancer.org/principal.php

Probe Explorer is an open access web-based bioinformatics application designed to show the association between microarray oligonucleotide probes and transcripts in the genomic context, but flexible enough to serve as a simplified genome and transcriptome browser. Coordinates and sequences of the genomic entities (loci, exons, transcripts), including vector graphics outputs, are provided for fifteen metazoa organisms and two yeasts. Alignment tools are used to built the associations between Affymetrix microarrays probe sequences and the transcriptomes (for human, mouse, rat and yeasts). Search by keywords is available and user searches and alignments on the genomes can also be done using any DNA or protein sequence query. Platform: Online tool

Proper citation: ProbeExplorer (RRID:SCR_007116) Copy   

•   Source: SciCrunch Registry

http://cello.life.nctu.edu.tw/

A subCELlular LOcalization predictor based on a multi-class support vector machine (SVM) classification system. CELLO uses 4 types of sequence coding schemes: the amino acid composition, the di-peptide composition, the partitioned amino acid composition and the sequence composition based on the physico-chemical properties of amino acids. They combine votes from these classifiers and use the jury votes to determine the final assignment.

Proper citation: CELLO (RRID:SCR_011968) Copy   

•   Source: SciCrunch Registry

http://iomics.us/

A genomics data analysis platform which generates decision models for healthcare organizations and medical research. This service is meant to utilize data through machine learning methods.

Proper citation: iOMICS (RRID:SCR_000239) Copy   

•   Source: SciCrunch Registry

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

Software application using a likelihood approach to inference of haplotype and nongenetic effects and their interactions in generalized linear models of disease penetrance, when haplotype phase is unknown for some subjects. Parameter estimates are obtained by use of an expectation-maximization (EM) algorithm and standard errors are calculated using Louis'' formula. (entry from Genetic Analysis Software)

Proper citation: R/HAPASSOC (RRID:SCR_009365) Copy   

•   Source: SciCrunch Registry

http://starbase.sysu.edu.cn/index.php

Web based tool to visualize, analyze, discover and download of large-scale functional genomics data. Used for analysis of the CLIP-Seq and Degradome-Seq data sets, exploration of miRNA–target interactions and decoding RNA interaction networks from CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data. To show RNA-RNA and protein-RNA interaction networks in developmental, physiological and pathological processes.

Proper citation: Starbase V2.0 (RRID:SCR_016303) 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