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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SIBLINK Resource Report Resource Website |
SIBLINK (RRID:SCR_009381) | software application, software resource | 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 | 2026-09-19 12:58:05 | 0 | ||||||||
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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 | 2026-09-19 12:58:07 | 261 | ||||||||
|
VISTA Browser Resource Report Resource Website 100+ 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 |
NHLBI ; Office of Biological and Environmental Research ; Office of Science ; US Department of Energy |
PMID:15215394 | Free, Freely available | OMICS_00948, biotools:vista | http://genome.lbl.gov/vista/index.shtml, https://bio.tools/vista | SCR_011808 | VISTA, vista | 2026-09-19 12:58:08 | 125 | |||||
|
SWEEP Resource Report Resource Website 10+ mentions |
SWEEP (RRID:SCR_009418) | SWEEP | software application, software resource | 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 | 2026-09-19 12:58:06 | 32 | ||||||||
|
SUMSTAT Resource Report Resource Website 10+ mentions |
SUMSTAT (RRID:SCR_009416) | software application, software resource | Software application that assess the joint disease association of multiple unlinked SNPs via sums of SNP specific test statistics. Genome-wide significance levels are obtained by per mutation analysis. (entry from Genetic Analysis Software) | gene, genetic, genomic, free pascal, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154663, biotools:sumstat | https://bio.tools/sumstat | SCR_009416 | 2026-09-19 12:58:06 | 11 | |||||||||
|
SUP Resource Report Resource Website |
SUP (RRID:SCR_009417) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May,6th, 2021. Software application as extension to SLINK/FastSLINK to allow more marker loci to be simulated in pedigrees conditional on trait values and in linkage equilibrium or disequilibrium with trait locus. entry from Genetic Analysis Software. | gene, genetic, genomic, c, c++, unix, linux, cygwin, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is related to: SLINK is related to: FASTSLINK is related to: bio.tools |
PMID:16803631 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154664, biotools:sup | https://bio.tools/sup | SCR_009417 | Slink Utility Program | 2026-09-19 12:58:06 | 0 | ||||||
|
SASGENE Resource Report Resource Website |
SASGENE (RRID:SCR_013084) | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 24,2023. SAS software program for gene segregation and linkage analysis in breeding population (entry from Genetic Analysis Software) | gene, genetic, genomic, sas, 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:sasgene, nlx_154608 | https://bio.tools/sasgene | SCR_013084 | 2026-09-19 12:58:09 | 0 | ||||||||
|
TASSEL Resource Report Resource Website 1000+ mentions |
TASSEL (RRID:SCR_012837) | TASSEL | software application, software resource | Software package which performs a variety of genetic analyses including association mapping, diversity estimation and calculating linkage disequilibrium. The association analysis between genotypes and phenotypes can be performed by either a general linear model or a mixed linear model. The general linear model now allows users to analyze complex field designs, environmental interactions, and epistatic interactions. The mixed model is specially designed to handle polygenic effects at multiple levels of relatedness including pedigree information. These new analyses should permit association analysis in a wide range plant and animal species. (entry from Genetic Analysis Software) | gene, genetic, genomic, java, web-based, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
nlx_154674, biotools:tassel | http://sourceforge.net/projects/tassel/, https://bio.tools/tassel | SCR_012837 | and Linkage, Trait Analysis by aSSociation, Evolution | 2026-09-19 12:58:08 | 2476 | |||||||
|
THESIAS Resource Report Resource Website 50+ mentions |
THESIAS (RRID:SCR_013449) | THESIAS | software application, software resource | Software program that performs haplotype-based association analysis in unrelated individuals. This program is based on a maximum likelihood model described in Tregouet et al. 2002 and is linked to the stochastic EM (SEM) algorithm. THESIAS allows the simultaneous estimation of haplotype frequencies and of their associated effects on the phenotype of interest. In its current version, both quantitative and qualitative phenotypes can be studied. Covariate-adjusted haplotype effects as well as haplotype x covariate interactions can be investigated. (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-windows, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btm058 | nlx_154102, OMICS_19747, biotools:tHESIAS | https://bio.tools/THESIAS, https://sources.debian.org/src/thesias/ | http://ecgene.net/genecanvas/downloads.php?cat_id=1 | SCR_013449 | Testing Haplotype EffectS In Association Studies | 2026-09-19 12:58:10 | 53 | |||||
|
ECLIPSE Resource Report Resource Website 100+ mentions |
ECLIPSE (RRID:SCR_013130) | software application, software resource | A set of three programs, preproc, eclipse2 and eclipse3 which analyze genetic marker data for genotypic errors and pedigree errors. Using a single preprocessing program (preproc), eclipse2 analyzes data on pairs of individuals, and eclise3 analyzes data jointly on trios. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, tested on, unix, (compaq tru64 v5.0a), bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:eclipse, nlx_154290 | https://bio.tools/eclipse | SCR_013130 | Error Correcting Likelihoods In Pedigree Structure Estimation. PANGAEA | 2026-09-19 12:58:09 | 124 | ||||||||
|
SNP HITLINK Resource Report Resource Website |
SNP HITLINK (RRID:SCR_013340) | SNP HITLINK | software application, software resource | Software program providing a useful pipeline to directly connect SNP data and linkage analysis program. SNP HiTLink currently supports the data from SNP chips provided by Affymetrix (Mapping 100k/500k array set, Genome-Wide Human SNP array 5.0/6.0) and Illumina (recently supported), carrying out typical linkage analysis programs of MLINK (FASTLINK/ LINKAGE package), Superlink, Merlin and Allegro. (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_154644, biotools:snp_hitlink | https://bio.tools/snp_hitlink | SCR_013340 | SNP HIgh-Throughput LINKage analysis system | 2026-09-19 12:58:09 | 0 | |||||||
|
PhyML Resource Report Resource Website 5000+ mentions |
PhyML (RRID:SCR_014629) | software resource, source code, web application | Web phylogeny server based on the maximum-likelihood principle. | phylogenic software, phylogeny, maximum likelihood, web server, bio.tools |
is used by: ProtTest is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite works with: PAML |
DOI:10.1093/molbev/msq060 | Public server, Source code is available on request | biotools:phyml, OMICS_04241 | https://bio.tools/phyml, https://sources.debian.org/src/phyml/ | SCR_014629 | 2026-09-19 12:58:12 | 7951 | |||||||
|
QmRLFS-finder Resource Report Resource Website 10+ mentions |
QmRLFS-finder (RRID:SCR_014584) | data analytics software, software application, software resource | A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis. | r-loop, r loop, rlf, rlfs, dna, rna, input sequences, output files, annotation, analysis, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
Singapore Agency for Science Technology and Research | PMID:26400173 PMID:25883153 |
Open Source | biotools:qmrlfs-finder | https://omictools.com/qmrlfs-finder-tool, https://bio.tools/qmrlfs-finder | SCR_014584 | QmRLFS finder | 2026-09-19 12:58:12 | 16 | |||||
|
FunRich: Functional Enrichment analysis tool Resource Report Resource Website 100+ mentions |
FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) | data analytics software, software application, software resource, standalone software | A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts. | network analysis, background database, charts, data analytics software, standalone software, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian |
PMID:25921073 PMID:26149235 |
Public, Open Source | biotools:funrich | https://bio.tools/funrich | SCR_014467 | 2026-09-19 12:58:12 | 431 | |||||||
|
MultiQC Resource Report Resource Website 1000+ mentions |
MultiQC (RRID:SCR_014982) | data access protocol, software resource | Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python. | bioinformatics, data aggregate, python, open source, html report, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Science for Life Laboratory ; National Genomics Infrastructure |
PMID:27312411 DOI:10.1093/bioinformatics/btw354 |
Open source, Available for download | biotools:multiqc, OMICS_12426 | https://github.com/ewels/MultiQC https://pypi.python.org/pypi/multiqc, https://bio.tools/multiqc, https://sources.debian.org/src/multiqc/ | SCR_014982 | 2026-09-19 12:58:13 | 3714 | ||||||
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topGO Resource Report Resource Website 1000+ mentions |
topGO (RRID:SCR_014798) | software resource, software toolkit | Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. | r, go, go graph, local similarities, software tool, software package, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite works with: Gene Ontology is hosted by: Bioconductor |
Available for download | biotools:topgo | https://bio.tools/topgo | SCR_014798 | 2026-09-19 12:58:12 | 3080 | ||||||||
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DANPOS2 Resource Report Resource Website 100+ mentions |
DANPOS2 (RRID:SCR_015527) | software resource, software toolkit | Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing. | nucleosome analysis, protein analysis, protein occupancy, bio.tools |
uses: Dpos is listed by: bio.tools is listed by: Debian |
Available for download, Different versions are available for download | biotools:danpos | https://bio.tools/danpos | SCR_015527 | DANPOS | 2026-09-19 12:58:13 | 114 | |||||||
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCRR KL2 RR029885; NIDDK P01 DK056492; NIDDK R01 DK088541; NIDDK RC4DK090860; NIGMS P50 GM071558; NLM RC2 LM010994 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-09-19 12:58:14 | 6 | ||||
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CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-09-19 12:58:15 | 1908 | ||||||
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Myriads Resource Report Resource Website 1+ mentions |
Myriads (RRID:SCR_017447) | data analytics software, software application, software resource | Software package for p value based multiple testing that also implements dependence test and p-value simulation. | P value, multiple, testing, simulation, BRAIN Initiative, bio.tools |
is recommended by: BRAIN Initiative is listed by: bio.tools is listed by: Debian |
NIMH MH111416 | PMID:29186285 | biotools:myriads | https://bio.tools/myriads | SCR_017447 | SGoF+ | 2026-09-19 12:58:16 | 1 |
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