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http://zfishbook.org/

Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.

Proper citation: zfishbook (RRID:SCR_006896) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/htqc/

A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc..

Proper citation: HTQC (RRID:SCR_006448) Copy   

•   Source: SciCrunch Registry

http://droog.gs.washington.edu/ldSelect.html

Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: LDSELECT (RRID:SCR_007010) Copy   

•   Source: SciCrunch Registry

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

Software application that is a faster version of SLINK (entry from Genetic Analysis Software)

Proper citation: FASTSLINK (RRID:SCR_008664) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/pedpeel/

Software program that prepares pedigree data for calculation of Elston-Stewarts'' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays (entry from Genetic Analysis Software)

Proper citation: PEDPEEL (RRID:SCR_008436) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/admixmap/index.html

General-purpose program for modelling admixture, using marker genotypes and trait data on a sample of individuals from an admixed population (such as African-Americans), where the markers have been chosen to have extreme differentials in allele frequencies between two or more of the ancestral populations between which admixture has occurred. The main difference between ADMIXMAP and classical programs for estimation of admixture such as ADMIX is that ADMIXMAP is based on a multilevel model for the distribution of individual admixture in the population and the stochastic variation of ancestry on hybrid chromosomes. This makes it possible to model the associations of ancestry between linked marker loci, and the association of a trait with individual admixture or with ancestry at a linked marker locus. (entry from Genetic Analysis Software)

Proper citation: ADMIXMAP (RRID:SCR_009035) Copy   

•   Source: SciCrunch Registry

http://mga.bionet.nsc.ru/soft/index.html

Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (entry from Genetic Analysis Software)

Proper citation: PEDIGREEQUERY (RRID:SCR_009041) Copy   

•   Source: SciCrunch Registry

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

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles.

Proper citation: MOSCPHASER (RRID:SCR_009092) 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.well.ox.ac.uk/~mfarrall/twoloc.htm

Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software)

Proper citation: TWOLOC (RRID:SCR_009230) Copy   

•   Source: SciCrunch Registry

http://www.daimi.au.dk/~mailund/GeneRecon/

Software application for linkage disequilibrium mapping using coalescent theory. It is based on a Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position. (entry from Genetic Analysis Software)

Proper citation: GENERECON (RRID:SCR_009195) 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

https://github.com/jdidion/atropos

Software tool for specific, sensitive, and speedy trimming of NGS reads.

Proper citation: Atropos (RRID:SCR_023962) Copy   

•   Source: SciCrunch Registry

https://code.google.com/archive/p/kempbasu/

Software package implements two significance tests for comparing digital gene expression profiles. They provide two programs: Kemp for the frequentist test and Basu for the Bayesian test, and some auxiliary scripts.

Proper citation: kempbasu (RRID:SCR_024055) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/placnet/

Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools.

Proper citation: Placnet (RRID:SCR_024176) Copy   

•   Source: SciCrunch Registry

https://prinseq.sourceforge.net/

Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format.

Proper citation: PRINSEQ (RRID:SCR_024178) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/poamsa/

Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.

Proper citation: POA (RRID:SCR_024172) Copy   

•   Source: SciCrunch Registry

https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index

Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.

Proper citation: PLIP (RRID:SCR_024173) Copy   

•   Source: SciCrunch Registry

https://github.com/Washington-University/CiftiLib

Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files.

Proper citation: CiftiLib (RRID:SCR_023996) Copy   

•   Source: SciCrunch Registry

https://github.com/rvaser/bioparser/

Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.

Proper citation: Bioparser (RRID:SCR_024065) Copy   

•   Source: SciCrunch Registry