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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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zfishbook Resource Report Resource Website 1+ mentions |
zfishbook (RRID:SCR_006896) | zfishbook | biomaterial supply resource, material resource | 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. | gene-breaking transposon, expression-tagged, revertible mutation, gene, transposon, mutation, mutant, brain, muscle, skin, secretory, cardiac, brain line, muscle line, skin line, secretory line, cardiac line, plasmid, expression, functional annotation, gene-breaking transposon line, gene-break transposon mutagenesis, cell line, annotation, embryonic zebrafish, larval zebrafish, bio.tools |
is listed by: One Mind Biospecimen Bank Listing is listed by: Debian is listed by: bio.tools is related to: Addgene is related to: Zebrafish International Resource Center has parent organization: Mayo Clinic Minnesota; Minnesota; USA |
Mayo Clinic Cancer Center ; Mayo Foundation ; NIGMS GM63904; NIDA DA14546; NHGRI HG006431 |
PMID:22067444 | Free, Freely available | biotools:zfishbook, nlx_151613 | https://bio.tools/zfishbook | SCR_006896 | book, z fish book, zfishbook, fish, z | 2026-08-07 09:26:25 | 4 | ||||
|
HTQC Resource Report Resource Website 10+ mentions |
HTQC (RRID:SCR_006448) | HTQC | software resource, software toolkit | A software toolkit including statistics tool for illumina high-throughput sequencing data, and filtration tools for sequence quality, length, tail quality, etc.. | c++, illumina, command-line |
is listed by: OMICtools is listed by: Debian has parent organization: SourceForge |
PMID:23363224 DOI:10.1186/1471-2105-14-33 |
GNU General Public License, v3 | OMICS_01052 | https://sources.debian.org/src/htqc/ | SCR_006448 | HTQC - Quality control and filtration for illumina sequencing data | 2026-08-07 09:26:20 | 43 | |||||
|
LDSELECT Resource Report Resource Website 10+ mentions |
LDSELECT (RRID:SCR_007010) | LDSELECT | software resource, software application | 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. | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ld_select, nlx_154426 | https://bio.tools/ld_select | SCR_007010 | 2026-08-07 09:26:29 | 15 | |||||||
|
FASTSLINK Resource Report Resource Website 10+ mentions |
FASTSLINK (RRID:SCR_008664) | FASTSLINK | software resource, software application | Software application that is a faster version of SLINK (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: SLINK is related to: SUP |
nlx_154312, biotools:snpcaller | https://bio.tools/snpcaller | SCR_008664 | faster SLINK | 2026-08-07 09:26:47 | 12 | |||||||
|
PEDPEEL Resource Report Resource Website |
PEDPEEL (RRID:SCR_008436) | PEDPEEL | software resource, software application | 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) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154524, biotools:pedpeel | https://bio.tools/pedpeel | SCR_008436 | 2026-08-07 09:26:46 | 0 | ||||||||
|
ADMIXMAP Resource Report Resource Website 10+ mentions |
ADMIXMAP (RRID:SCR_009035) | ADMIXMAP | software resource, software application | 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) | gene, genetic, genomic, c++, linux, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_153999, biotools:admixmap | https://bio.tools/admixmap | SCR_009035 | Admixture mapping | 2026-08-07 09:26:51 | 20 | |||||||
|
PEDIGREEQUERY Resource Report Resource Website 1+ mentions |
PEDIGREEQUERY (RRID:SCR_009041) | PEDIGREEQUERY | software resource, software application | 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) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154007, biotools:pedcut | https://bio.tools/pedcut | SCR_009041 | 2026-08-07 09:26:51 | 1 | ||||||||
|
MOSCPHASER Resource Report Resource Website |
MOSCPHASER (RRID:SCR_009092) | MOSCPHASER | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 29, 2016. Software application for inferring haplotypes composed of both CNV alleles and SNP alleles. | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
PMID:18492685 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154109, biotools:mocsphaser | https://bio.tools/mocsphaser | http://emu.src.riken.jp/MOCSphase/MOSCphaser.zip | SCR_009092 | Mixture Of Cnv-Snp PHASER | 2026-08-07 09:26:53 | 0 | ||||
|
GLUE Resource Report Resource Website 10+ mentions |
GLUE (RRID:SCR_009211) | GLUE | software resource, software application | 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. | gene, genetic, genomic, perl, any web browser, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154360, biotools:GLUE | https://bio.tools/GLUE | http://portal.litbio.org/Registered/Webapp/glue/ | SCR_009211 | Genetic Linkage User Environment | 2026-08-07 09:26:54 | 46 | |||||
|
TWOLOC Resource Report Resource Website |
TWOLOC (RRID:SCR_009230) | TWOLOC | software resource, software application | Software package for analyzing two-locus susceptibility gene models in affected sib-pair data (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran77, pascal, awk, unix, (saloris/dec unix/irix/..), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154387, biotools:twoloc | https://bio.tools/twoloc | SCR_009230 | 2026-08-07 09:26:55 | 0 | ||||||||
|
GENERECON Resource Report Resource Website 1+ mentions |
GENERECON (RRID:SCR_009195) | GENERECON | software resource, software application | 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) | gene, genetic, genomic, c++, unix, linux, macos, ms-windows, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154338, biotools:generecon | https://bio.tools/generecon | SCR_009195 | 2026-08-07 09:26:59 | 1 | ||||||||
|
HTR Resource Report Resource Website 1+ mentions |
HTR (RRID:SCR_009241) | HTR | software resource, software application | 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) | gene, genetic, genomic, c++, bash shell, ms-windows, unix, solaris, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154402, biotools:htr | https://bio.tools/htr | SCR_009241 | Haplotype Trend Regression | 2026-08-07 09:27:00 | 1 | |||||||
|
Atropos Resource Report Resource Website 1+ mentions |
Atropos (RRID:SCR_023962) | software resource, software application, source code | Software tool for specific, sensitive, and speedy trimming of NGS reads. | speedy trimming of NGS reads, NGS reads, Next Generation Sequencing, | is listed by: Debian | PMID:28875074 | Free, Available for download, Freely available | OMICS_20869 | https://sources.debian.org/src/atropos/ | SCR_023962 | atropos | 2026-08-07 09:30:02 | 3 | ||||||
|
kempbasu Resource Report Resource Website |
kempbasu (RRID:SCR_024055) | software resource, software toolkit | 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. | comparing digital gene expression profiles, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/kempbasu/ | SCR_024055 | 2026-08-07 09:30:09 | 0 | |||||||||
|
Placnet Resource Report Resource Website |
Placnet (RRID:SCR_024176) | software library, software resource, software toolkit | 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. | plasmid constellation networks, identifies splasmids, visualizes and analyzes plasmids, WGS projects, creating network of contig interactions, comprehensive plasmid analysis within WGS datasets, | is listed by: Debian | PMID:25522143 | Free, Available for download, Freely available, | OMICS_11487 | https://sources.debian.org/src/placnet/ | SCR_024176 | plasmid constellation networks, placnet | 2026-08-07 09:30:11 | 0 | ||||||
|
PRINSEQ Resource Report Resource Website 100+ mentions |
PRINSEQ (RRID:SCR_024178) | software library, software resource, software toolkit | 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. | data quality control, data preprocessing, genomic and metagenomic datasets, | is listed by: Debian | PMID:21278185 | Free, Available for download, Freely available, | https://sources.debian.org/src/prinseq-lite/ | SCR_024178 | prinseq-lite | 2026-08-07 09:30:12 | 113 | |||||||
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POA Resource Report Resource Website |
POA (RRID:SCR_024172) | software library, software resource, software toolkit | Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment. | sequence alignment, multiple sequence alignment, handle branching in alignment, handle indels in alignment, | is listed by: Debian | DOI:10.1093/bioinformatics/bth126 | Free, Available for download, Freely available, | OMICS_14254 | https://sources.debian.org/src/poa/ | SCR_024172 | poa, Partial Order Alignment | 2026-08-07 09:30:11 | 0 | ||||||
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PLIP Resource Report Resource Website 100+ mentions |
PLIP (RRID:SCR_024173) | software library, software resource, software toolkit | 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. | Protein Ligand Interaction Profiler, | is listed by: Debian | DOI:10.1093/nar/gkv315 | Free, Available for download, Freely available, | OMICS_08028 | https://sources.debian.org/src/plip/, https://github.com/pharmai/plip | SCR_024173 | Protein-Ligand Interaction Profiler, plip | 2026-08-07 09:30:06 | 226 | ||||||
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CiftiLib Resource Report Resource Website |
CiftiLib (RRID:SCR_023996) | software library, software resource, software toolkit | Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files. | C++, reading and writing files, CIFTI-2, CIFTI-1 | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ciftilib/ | SCR_023996 | ciftilib | 2026-08-07 09:30:02 | 0 | ||||||||
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Bioparser Resource Report Resource Website 1+ mentions |
Bioparser (RRID:SCR_024065) | software library, software resource, software toolkit | 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. | C ++, parsing formats, FASTA/Q, MHAP/PAF/SAM, support for zlib compressed files, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbioparser-dev/ | SCR_024065 | bioparser, libbioparser-dev | 2026-08-07 09:30:04 | 3 |
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