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http://www-gene.cimr.cam.ac.uk/clayton/software/

Software program for estimating frequencies of haplotypes of large numbers of diallelic markers from unphased genotype data from unrelated subjects (entry from Genetic Analysis Software)

Proper citation: SNPHAP (RRID:SCR_008456) Copy   

•   Source: SciCrunch Registry

http://www.phenote.org/

Phenote is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface and infrastructure to record genotype-phenotype pairs, together with the provenance for the annotation. Typical users of Phenote include literature curators, laboratory researchers, and clinicians looking for a method to record data in a user-friendly and computable way. Features of Phenote include the use of any OBO-format ontology, ontology navigation and term information display, bulk sort, copy, edit, and delete of phenotype-genotype character entries, and a variety of export formats. Phenote is a project of the Berkeley Bioinformatics Open-Source Projects (BBOP).

Proper citation: Phenote: A Phenotype Annotation Tool using Ontologies (RRID:SCR_008334) Copy   

•   Source: SciCrunch Registry

http://cmpg.unibe.ch/software/simcoal/

Software application (entry from Genetic Analysis Software)

Proper citation: SIMCOAL (RRID:SCR_008450) Copy   

•   Source: SciCrunch Registry

http://dicom.offis.de/dcmtk.php.en

Software collection of libraries and applications implementing large parts of DICOM standard for medical image communication.Includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over network connection, as well as demonstrative image storage and worklist servers.

Proper citation: DCMTK: DICOM Toolkit (RRID:SCR_007360) Copy   

•   Source: SciCrunch Registry

http://biomail.sourceforge.net/biomail/

BioMail is a small web-based application for medical researchers, biologists, and anyone who wants to know the latest information about a disease or a biological phenomenon. It is written to automate searching for recent scientific papers in the PubMed Medline database. BioMail is free and will stay free. What does BioMail do? Periodically BioMail does a user-customized Medline search and sends all matching articles recently added to Medline to the users'' e-mail address. HTML-formatted e-mails generated by BioMail can be used to view selected references in medline format (compatible with most reference manager programs). Why is BioMail helpful? If you use Medline, it may be hard to remember when you did your last search. Often you must scan titles you have already seen to be certain you didn''t miss an important reference. BioMail will perform routine searches for you. This program alerts users to all new papers in their fields automatically. It also helps the user to ''refine'' search patterns once and for all. There is no need to wonder: ''What was that great search pattern I used last Saturday?''. All patterns are safe in the database and can be accessed, tuned, or deleted any time. It is also useful for countries where access to the Internet is not yet widely available. If a person has a permanent e-mail address, but only sporadic www access, she/he only needs to fill out a BioMail form once and then will receive new references from Medline continually.

Proper citation: BioMail (RRID:SCR_008174) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: RVTESTS (RRID:SCR_007639) Copy   

•   Source: SciCrunch Registry

http://watson.hgen.pitt.edu/register/soft_doc.html,

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application that assigns each person the haplotype with the highest conditional probability using Elston-Stewart algorithm (entry from Genetic Analysis Software)

Proper citation: HAPLO 1 (RRID:SCR_009058) Copy   

•   Source: SciCrunch Registry

http://www.genetics.emory.edu/labs/epstein/software/scout/index.html

Software program for conducting combined association analysis of triads and unrelated subjects (entry from Genetic Analysis Software)

Proper citation: SCOUT (RRID:SCR_009054) Copy   

•   Source: SciCrunch Registry

http://www.cs.helsinki.fi/group/genetics/haplotyping.html

Software application for population-based haplotyping (entry from Genetic Analysis Software)

Proper citation: HAPLOREC (RRID:SCR_009055) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software for segregation and pathway analysis.

Proper citation: SEGPATH (RRID:SCR_009052) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application to calculate kinship coefficient or coefficient of coancestry (the probability that alleles at a given locus are identical by descent).

Proper citation: KIN (RRID:SCR_009047) Copy   

•   Source: SciCrunch Registry

http://www.hoschl.cz/faster/

Software application to reduce family members so the families can be used in GENEHUNTER program. FASTER eliminates the most redundant individuals according to the set of weights (preferences) (Age, Information about genetic Markers, etc.) The program has several features such as automatical reducement of branches without any affected individuals, etc. (entry from Genetic Analysis Software)

Proper citation: FASTER (RRID:SCR_009045) Copy   

•   Source: SciCrunch Registry

http://www.multiqtl.com/

Software application that integrates a broad spectrum of data mining, statistical analysis, interactive visualization and modeling tools that allow QTL analysis based on advanced and sophisticated methods for maximum extraction of the mapping information from data. (entry from Genetic Analysis Software)

Proper citation: MULTIQTL (RRID:SCR_009043) Copy   

•   Source: SciCrunch Registry

http://galton.uchicago.edu/~mcpeek/software/spermseg

Software application for analysis of segregation in single-sperm data (entry from Genetic Analysis Software)

Proper citation: SPERMSEG (RRID:SCR_009044) Copy   

•   Source: SciCrunch Registry

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

Software application (entry from Genetic Analysis Software)

Proper citation: ALLASS (RRID:SCR_009040) Copy   

•   Source: SciCrunch Registry

http://gmc.mdc-berlin.de/alohomora/

Software application designed to facilitate genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as the Affymetrix GeneChip(R) Human Mapping 10K Array. (entry from Genetic Analysis Software)

Proper citation: ALOHOMORA (RRID:SCR_009117) Copy   

•   Source: SciCrunch Registry

http://www.hgu.mrc.ac.uk/Softdata/ALP/

Microsoft Windows application designed to analyze microsatellite DNA fragments separated on an Automated Laser Fluorescence sequencer. (entry from Genetic Analysis Software)

Proper citation: ALP (RRID:SCR_009118) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A tool designed to help visualize the joint effect of genes and continuous environmental covariates on complex human disease simulation models.

Proper citation: SIMULAPLOT (RRID:SCR_009079) Copy   

•   Source: SciCrunch Registry

http://www.stat.uchicago.edu/~wen/tuna/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 22, 2016. Free software package for estimating allele frequencies for all the SNPs available in a population reference panel (e.g. HapMap data base) based on genotype data from a subset of markers (e.g. the Illumina HumanHap300 BeadChip SNP set) in a group of subjects (e.g. the cases in a case-control sample)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TUNA (RRID:SCR_009112) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/caspar.html

Software application who''s main novel feature is conditional linkage analyses, in which the population can be subdivided according to criteria at some loci and analyzed for linkage at other loci. CASPAR uses simulation to overcome the problems inherent in such multiple testing. (entry from Genetic Analysis Software)

Proper citation: CASPAR (RRID:SCR_009074) Copy   

•   Source: SciCrunch Registry