Tools   Select Another Resource Report Type

http://www.reading.ac.uk/Statistics/genetics/software.html

Software application (entry from Genetic Analysis Software)

Proper citation: LDMET (RRID:SCR_001127) Copy   

•   Source: SciCrunch Registry

http://support.illumina.com/sequencing/sequencing_software/casava.html

Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting

Proper citation: CASAVA (RRID:SCR_001802) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/Polymutt

Software program that implemented a likelihood-based framework for calling single nucleotide variants and detecting de novo point mutation events in families for next-generation sequencing data. The program takes as input genotype likelihood format (GLF) files which can be generated following the Creation of GLF files instruction and outputs the result in the (VCF) format. The variant calling and de novo mutation detection are modelled jointly within families and can handle both nuclear and extended pedigrees without consanguinity loops. The input is a set of GLF files for each of family members and the relationships are specified through the .ped file. (entry from Genetic Analysis Software)

Proper citation: POLYMUTT (RRID:SCR_002051) Copy   

•   Source: SciCrunch Registry

https://hsph.harvard.edu/research/price-lab/software/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: EIGENSOFT/EIGENSTRAT (RRID:SCR_001357) Copy   

•   Source: SciCrunch Registry

https://www.broadinstitute.org/birdsuite/birdsuite

Open-source set of tools to detect and report SNP genotypes, common Copy-Number Polymorphisms (CNPs), and novel, rare, or de novo CNVs in samples processed with the Affymetrix platform. While most of the components of the suite can be run individually (for instance, to only do SNP genotyping), the Birdsuite is especially intended for integrated analysis of SNPs and CNVs.

Proper citation: BIRDSUITE (RRID:SCR_001794) 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://genome.sph.umich.edu/wiki/PedScript

Software tool that allows scripting of simple modifications to pedigree files. (entry from Genetic Analysis Software)

Proper citation: PEDSCRIPT (RRID:SCR_004571) Copy   

•   Source: SciCrunch Registry

http://www.chg.duke.edu/software/pedplot.html

Pedigree Plotting Program for the Pedfile Format (entry from Genetic Analysis Software)

Proper citation: PEDPLOT (RRID:SCR_003843) Copy   

•   Source: SciCrunch Registry

http://www.stats.ox.ac.uk/~marchini/software.html

A R package for assessing the power of genome-wide association studies using commercially available genotyping chips. The package encapsulates extensive simulation results generated by our program HAPGEN. (entry from Genetic Analysis Software)

Proper citation: GWAPOWER (RRID:SCR_009216) Copy   

•   Source: SciCrunch Registry

https://academic.oup.com/bioinformatics/article/21/24/4430/180359

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 7,2025. Software application that is a rank-based meta-analysis method for analyzing results from genome-wide linkage searches. A software package is now available. The gsma software calculates the summed rank for any number of studies and bins, then obtains p-values for the Summed Rank and the Ordered Rank statistics, by simulation. Weighted and unweighted analyses are performed. A test data set is included. (entry from Genetic Analysis Software)

Proper citation: GSMA (RRID:SCR_009214) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 6, 2016. A web interface to several commonly used statistical genetics programs, including Linkage, Genehunter, Merlin, Unphased, and Transmit. It simplifies their use through graphical selection of program options, automation of multiple analyses, and viewing of graphical output. GLUE is available to HGMP account holders; registration is free to all academic users., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GLUE (RRID:SCR_009211) Copy   

•   Source: SciCrunch Registry

http://www.sph.umich.edu/csg/chen/ghost/

Software package for family-based genomewide association (GWA) analysis, with the ability to infer missing genotypes using the Elston-Stewart algorithm. When SNPs from an association panel are less complete (i.e., having more missing genotypes) than markers from a linkage panel, many of the missing genotypes can be determined. GHOST can handle large pedigrees -- when pedigrees are small, Merlin is also recommended for this analysis. (entry from Genetic Analysis Software)

Proper citation: GHOST (RRID:SCR_009209) Copy   

•   Source: SciCrunch Registry

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

Software application for analysis and manipulation of genetic linkage data of genetic linkage data, including conversions of pedigree files between CRI-MAP and LINKAGE format. (entry from Genetic Analysis Software)

Proper citation: GENTOOLS (RRID:SCR_009205) Copy   

•   Source: SciCrunch Registry

http://lbm.ab.a.u-tokyo.ac.jp/~ukai/gest98.html

Software application (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GEST (RRID:SCR_009206) Copy   

•   Source: SciCrunch Registry

http://www.genoproof.com or http://qualitype.de/genoproof/

Software package for the analysis of multiplex PCR kits within the scope of paternity testing, kinship cases and population studies. GenoProof offers: (1) probably the most extensive existing population database for all supported markers of more than 50 ethnic groups, (2) individually configurable quality assurance options, (3) complex concept of user rights in order to guarantee data security, (4) languages German and English (entry from Genetic Analysis Software)

Proper citation: GENOPROOF (RRID:SCR_009204) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/resources/software/genevar/

A database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression in eQTL studies. Genevar allows researchers to investigate eQTL (expression quantitative trait loci) associations within a gene locus of interest in real time. The database and application can be installed on a standard computer in database mode and, in addition, on a server to share discoveries among affiliations or the broader community over the internet via web services protocols. (entry from Genetic Analysis Software)

Proper citation: GENEVAR (RRID:SCR_009201) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.ust.hk/MegaSNPHunter.html

Software application that takes case-control genotype data as input and produces a ranked list of multi-SNP interactions. In particular, the whole genome is first partitioned into multiple short subgenomes and a boosting tree classifier is built for each subgenomes based on multi-SNP interactions and then used to measure the importance of SNPs. The method keeps relatively more important SNPs from all subgenomes and let them compete with each other in the same way at the next level. The competition terminates when the number of selected SNPs is less than the size of a subgenome. (entry from Genetic Analysis Software)

Proper citation: MEGASNPHUNTER (RRID:SCR_009287) Copy   

•   Source: SciCrunch Registry

http://carlit.toulouse.inra.fr/MCQTL/

Software package to perform QTL mapping in multi-cross designs that allows the analysis of the usual populations derived from inbred lines and can link the families by assuming that the QTL locations are the same in all them. Moreover, a diallel modelling of the QTL genotypic effects is allowed in multiple related families. Obviously, the analysis of a single cross is also feasible. (entry from Genetic Analysis Software)

Proper citation: MCQTL (RRID:SCR_009285) Copy   

•   Source: SciCrunch Registry

http://www-genome.wi.mit.edu/genome_software

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23,2022. Software application (entry from Genetic Analysis Software)

Proper citation: MAPMAKER/QTL (RRID:SCR_009283) Copy   

•   Source: SciCrunch Registry