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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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EHRtemporalVariability Resource Report Resource Website 1+ mentions |
EHRtemporalVariability (RRID:SCR_018663) | software resource, software application, data processing software | Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users. | Delineating temporal data set shift, data set shift, electronic health record, temporal variability, delineate temporal data set shift, data dissimilarities, reliable data reuse, examine data set, biomedical data reuse, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: CRAN is related to: Shiny |
DOI:10.1101/2020.04.07.20056564 | Free, Available for download, Freely available | biotools:ehrtemporalvariability | https://cran.r-project.org/web/packages/EHRtemporalVariability/readme/README.html, https://bio.tools/ehrtemporalvariability | SCR_018663 | Electronic Health Records temporal variability | 2026-08-01 12:08:50 | 3 | ||||||
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PyBEL Resource Report Resource Website 1+ mentions |
PyBEL (RRID:SCR_017660) | software resource, software toolkit | Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J. | Parsing, validating, compiling, converting, network, BEL, biological, expression, language, bio.tools |
is used by: Bio2BEL is listed by: bio.tools is listed by: Debian is related to: Biological Expression Language |
European Union/European Federation of Pharmaceutical Industries and Associations (EFPIA) Innovative Medicines Initiative Joint Undertaking | PMID:29048466 | Free, Available for download, Freely available | biotools:pybel, SCR_024180 | https://github.com/pybel/pybel, https://bio.tools/pybel/, https://pybel.readthedocs.io | https://sources.debian.org/src/python3-pybel/ | SCR_017660 | pybel, Python Biological Expression Language | 2026-08-01 12:08:44 | 1 | ||||
|
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 | 2026-08-01 12:10:52 | 1 | ||||||||
|
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 | 2026-08-01 12:10:51 | 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 | 2026-08-01 12:10:53 | 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 | 2026-08-01 12:10:54 | 19 | |||||||
|
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 | 2026-08-01 12:10:44 | 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 | 2026-08-01 12:10:46 | 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 | 2026-08-01 12:10:55 | 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 | 2026-08-01 12:10:55 | 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 | 2026-08-01 12:10:56 | 1 | |||||||
|
SKAT Resource Report Resource Website 100+ mentions |
SKAT (RRID:SCR_009396) | software resource, software application | Software application that is a SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies. (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_154634, biotools:skat | https://bio.tools/skat | SCR_009396 | SNP-set (Sequence) Kernel Association Test | 2026-08-01 12:11:00 | 273 | ||||||||
|
MULTIDISEQ Resource Report Resource Website |
MULTIDISEQ (RRID:SCR_009304) | MULTIDISEQ | software resource, software application | A multipoint linkage analysis software which allows Marker-Marker LD (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_154494, biotools:multidiseq | https://bio.tools/multidiseq | SCR_009304 | 2026-08-01 12:10:59 | 0 | ||||||||
|
MPDA Resource Report Resource Website 10+ mentions |
MPDA (RRID:SCR_009303) | MPDA | software resource, software application | A tool for analyzing hybridization intensity data from microarray-based pooled DNA experiments. MPDA was developed under the software platform, MATLABR, and provided user-friendly interfaces adapted to Windows systems (Windows 98, Windows 2000 and Windows XP). or users without installing software MATLABR, we also developed stand-alone executables generated via the MATLABR compiler. MPDA provides four major functions: (1) Whole-genome DNA amplification/hybridization analysis, (2) Allele frequency estimation, (3) Association mapping, (4) Allelic imbalance detection. Graphic and numerical outputs from MPDA support global and detailed inspection for bulk of genomic data. (entry from Genetic Analysis Software) | gene, genetic, genomic, matlabr, ms-windows, (windows98/2000/xp), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:mpda, nlx_154492 | https://bio.tools/mpda | SCR_009303 | Microarray Pooled DNA Analyser | 2026-08-01 12:10:48 | 12 | |||||||
|
SIMPED Resource Report Resource Website 1+ mentions |
SIMPED (RRID:SCR_009388) | software resource, software application | Software program that quickly generates haplotypes and/or genotype data for a large number of marker loci (>20,000) for pedigrees of virtually any size and complexity. Haplotypes and/or genotypes are generated using user specified genetic map distances and haplotypes and/or allele frequencies. (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, ms-window, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:simped, nlx_154627 | https://bio.tools/simped | http://www.hgsc.bcm.tmc.edu/genemapping | SCR_009388 | 2026-08-01 12:11:00 | 1 | ||||||||
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SIBLINK Resource Report Resource Website |
SIBLINK (RRID:SCR_009381) | software resource, software application | Software application that allows the user to perform multipoint linkage analysis based on estimated IBD sharing between affected sibpairs. IBD sharing is inferred from IBS status, given marker genotypes, frequencies, and locations. Resulting LOD scores are maximized across a grid of possible disease locations and IBD sharing vectors. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, solaris, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:siblink, nlx_154616 | https://bio.tools/siblink | http://wwwchg.duhs.duke.edu/software/siblink.html | SCR_009381 | 2026-08-01 12:10:50 | 0 | ||||||||
|
mothur Resource Report Resource Website 5000+ mentions |
mothur (RRID:SCR_011947) | software resource, software application, standalone software | An open-source software package for describing and comparing microbial communities. It incorporates the functionality of a number of computational tools, calculators, and visualization tools. | microbiome, microbial ecology, open source, bioinformatics, standalone software |
is used by: Nephele is listed by: OMICtools is listed by: Human Microbiome Project is listed by: Debian |
DOI:10.1128/AEM.01541-09 | Open source | OMICS_01518 | https://github.com/mothur/mothur/releases/tag/v1.38.1.1, https://sources.debian.org/src/mothur/ | SCR_011947 | 2026-08-01 12:10:52 | 5851 | |||||||
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Bioinformatics Toolkit Resource Report Resource Website 100+ mentions |
Bioinformatics Toolkit (RRID:SCR_010277) | software resource, software toolkit | A platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. Most frequently used tools HHpred Sensitive protein homology detection and structure prediction by HMM-HMM-comparison. Starting from a query sequence, HHpred builds a multiple sequence alignment using HHblits and turns it into a profile HMM. This is then compared it with a database of HMMs representing proteins with known structure (e.g. PDB, SCOP) or annotated protein families (e.g. PFAM, SMART, CDD, COGs, KOGs). The output is a list of closest homologs with alignments. HHpred can also build 3d homology models using the identified templates in the PDB database. It can optimize template picking and query-template alignments for homology modeling. The HHblits software is part of the open source package HHsuite. HHblits Remote homology detection method based on iterative HMM-HMM comparison. HHblits can build high-quality MSAs starting from single sequences or from MSAs. It transforms these into a query HMM and iteratively searches through uniprot20 or nr20 databases by adding significantly similar sequences from the previous search to the updated query HMM for the next search iteration. Compared to PSI-BLAST, HHblits is faster, up to twice as sensitive and produces more accurate alignments. The HHblits software is part of the open source package HHsuite. Quick2d Quick2D gives you an overview of secondary structure features like alpha-helices, extended beta-sheets, coiled coils, transmembrane helices and disorder regions. Predictions by PSIPRED, JNET, Prof(Rost), Prof(Ouali), Coils, MEMSAT2, HMMTOP, DISOPRED2 and VSL2. Modeller A Program for Comparative Protein Structure Modelling by Satisfaction of Spatial Restraints. Coils/PCoils This server compares a single sequence (COILS) or a sequence alignment (PCOILS) to a database of known coiled-coils and derives a similarity score. The program then calculates the probability that the sequence will adopt a coiled-coil conformation. PSI-Blast Search with an amino acid sequence against protein databases for locally similar sequences. Similar to ProteinBLAST but more sensitive. PSI-BLAST first performs a BLAST search and builds an alignment from the best local hits. This alignment is then used as a query for the next round of search. After each successive round the search alignment is updated. | bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
DOI:10.1038/NMETH.1818 | nlx_156936, OMICS_28407, biotools:bioinformatics_toolkit | https://bio.tools/bioinformatics_toolkit, https://sources.debian.org/src/hhsuite/ | SCR_010277 | 2026-08-01 12:11:00 | 235 | ||||||||
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VISTA Browser Resource Report Resource Website 50+ mentions |
VISTA Browser (RRID:SCR_011808) | software resource, software toolkit | Software tools for comparative genomics.Comprehensive suite of programs and databases for comparative analysis of genomic sequences. There are two ways of using VISTA - you can submit your own sequences and alignments for analysis (VISTA servers) or examine pre-computed whole-genome alignments of different species. | Comparative genomics tools, genomic sequences, comparative analysis, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
Office of Biological and Environmental Research ; Office of Science ; US Department of Energy ; NHLBI |
PMID:15215394 | Free, Freely available | OMICS_00948, biotools:vista | http://genome.lbl.gov/vista/index.shtml, https://bio.tools/vista | SCR_011808 | VISTA, vista | 2026-08-01 12:11:02 | 87 | |||||
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SWEEP Resource Report Resource Website 10+ mentions |
SWEEP (RRID:SCR_009418) | SWEEP | software resource, software application | Software application that allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype test to look for alleles of high frequency with long-range linkage disequilibrium, which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers. SWEEP takes phased genotype data as input, detects all haplotype blocks in that data, and then determines the frequency and long-range LD for each allele in each block. (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 |
biotools:sweep, nlx_154667 | https://bio.tools/sweep | SCR_009418 | 2026-08-01 12:10:51 | 32 |
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