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http://balance.med.utah.edu/wiki/index.php/JPSGCS

Software application to address problems in statistical genetics; however, they include several programs and packages that may be more generally useful, for instance, programs to draw and manipulate graphs, simulation programs, and programs to estimate graphical models. (entry from Genetic Analysis Software)

Proper citation: JPSGCS (RRID:SCR_009249) Copy   

•   Source: SciCrunch Registry

http://cedar.genetics.soton.ac.uk/pub/PROGRAMS/nopar

Software application for non-parametric linkage and association tests primarily for a quantitative trait (entry from Genetic Analysis Software)

Proper citation: NOPAR (RRID:SCR_009246) Copy   

•   Source: SciCrunch Registry

http://statgen.ncsu.edu/zaykin/htr.html

Software application for haplotype association mapping using unrelated individuals; fixed and sliding window analysis; overall tests and tests for individual haplotype effects (entry from Genetic Analysis Software)

Proper citation: HTR (RRID:SCR_009241) Copy   

•   Source: SciCrunch Registry

http://lbm.ab.a.u-tokyo.ac.jp/software.html

Software programs that allow a user to get results on segregation ratio, linkage test, recombination value, grouping of markers, ordering of markers by metric multidimensional scaling, drawing map and graphical genotype. ALso QTL analysis by interval mapping and ANOVA are possible. (entry from Genetic Analysis Software)

Proper citation: MAPL (RRID:SCR_009278) Copy   

•   Source: SciCrunch Registry

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   

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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   

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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://metscape.ncibi.org

A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.

Proper citation: Metscape (RRID:SCR_014687) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/collaboration/sequencing-idd-regions-nod-mouse-genome/

Genetic variations associated with type 1 diabetes identified by sequencing regions of the non-obese diabetic (NOD) mouse genome and comparing them with the same areas of a diabetes-resistant C57BL/6J reference mouse allowing identification of single nucleotide polymorphisms (SNPs) or other genomic variations putatively associated with diabetes in mice. Finished clones from the targeted insulin-dependent diabetes (Idd) candidate regions are displayed in the NOD clone sequence section of the website, where they can be downloaded either as individual clone sequences or larger contigs that make up the accession golden path (AGP). All sequences are publicly available via the International Nucleotide Sequence Database Collaboration. Two NOD mouse BAC libraries were constructed and the BAC ends sequenced. Clones from the DIL NOD BAC library constructed by RIKEN Genomic Sciences Centre (Japan) in conjunction with the Diabetes and Inflammation Laboratory (DIL) (University of Cambridge) from the NOD/MrkTac mouse strain are designated DIL. Clones from the CHORI-29 NOD BAC library constructed by Pieter de Jong (Children's Hospital, Oakland, California, USA) from the NOD/ShiLtJ mouse strain are designated CHORI-29. All NOD mouse BAC end-sequences have been submitted to the International Nucleotide Sequence Database Consortium (INSDC), deposited in the NCBI trace archive. They have generated a clone map from these two libraries by mapping the BAC end-sequences to the latest assembly of the C57BL/6J mouse reference genome sequence. These BAC end-sequence alignments can then be visualized in the Ensembl mouse genome browser where the alignments of both NOD BAC libraries can be accessed through the Distributed Annotation System (DAS). The Mouse Genomes Project has used the Illumina platform to sequence the entire NOD/ShiLtJ genome and this should help to position unaligned BAC end-sequences to novel non-reference regions of the NOD genome. Further information about the BAC end-sequences, such as their alignment, variation data and Ensembl gene coverage, can be obtained from the NOD mouse ftp site.

Proper citation: Sequencing of Idd regions in the NOD mouse genome (RRID:SCR_001483) Copy   

•   Source: SciCrunch Registry

http://www.chickest.udel.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28,2025. A chicken EST Web site has been created to provide access to the data, and a set of unique sequences has been deposited with GenBank. This site contains over 40,000 EST sequences from the chicken cDNA libraries in the University of Delaware collection. Users can perform keyword searches, BLAST nucleotide sequences against our database, view clusters of similar or overlapping clones, and order clones. The cDNA and gene sequences of many mammalian cytokines and their receptors are known. However, corresponding information on avian cytokines is limited due to the lack of cross-species activity at the functional level or strong homology at the molecular level. To improve the efficiency of identifying cytokines and novel chicken genes, a directionally cloned cDNA library from T-cell-enriched activated chicken splenocytes was constructed, and the partial sequence of 5251 clones was obtained. Sequence clustering indicates that 2357 (42%) of the clones are present as a single copy, and 2961 are distinct clones, demonstrating the high level of complexity of this library. Comparisons of the sequence data with known DNA sequences in GenBank indicate that approximately 25% of the clones match known chicken genes, 39% have similarity to known genes in other species, and 11% had no match to any sequence in the database. Several previously uncharacterized chicken cytokines and their receptors were present in our library. This collection provides a useful database for cataloging genes expressed in T cells and a valuable resource for future investigations of gene expression in avian immunology. Therefore, the Chick EST database was created.

Proper citation: UD Chick EST Project (RRID:SCR_002236) Copy   

•   Source: SciCrunch Registry

http://soap.genomics.org.cn/

Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SOAP (RRID:SCR_000689) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/DGCA/versions/1.0.2

Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.

Proper citation: Differential Gene Correlation Analysis (RRID:SCR_020964) Copy   

•   Source: SciCrunch Registry

http://faryabi05.med.upenn.edu:8050/

Portal for scRNA-seq study. Includes dendrogram visualization and clustering of all cells in scRNA-seq study as well as interactive filtered views for cell type, gene and/or donor group.

Proper citation: Mapping the pancreas and its ecosystem at the cellular level in health and type 1 diabetes (RRID:SCR_020952) Copy   

•   Source: SciCrunch Registry