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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MetaP Resource Report Resource Website 10+ mentions |
MetaP (RRID:SCR_014686) | computational hosting, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 5,2023. Software tool for processing in metabolomics experiments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | metabolomics, metabolomics tool, server, data analysis, processing, computational hosting, bio.tools |
is listed by: Metabolomics Workbench is listed by: bio.tools |
DOI:10.1155/2011/839862 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:metap | https://bio.tools/metap | SCR_014686 | metap, MetaP Server | 2026-08-03 09:35:50 | 14 | ||||||
|
TomoMiner Resource Report Resource Website 1+ mentions |
TomoMiner (RRID:SCR_015045) | software resource, source code | Software platform for large-scale cryo electron subtomogram classification, alignment, and averaging. | analysis platform, cryo electron subtomogram, subtomogram classification, subtomogram alignment, subtomogram averaging, subtomogram analysis, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA requires: Python Programming Language requires: NumPy requires: SciPy requires: LAPACK linear algebra library requires: Cython C-Extensions for Python |
Available for download | biotools:tomominer | https://bio.tools/tomominer | SCR_015045 | 2026-08-03 09:35:59 | 3 | ||||||||
|
FastTree Resource Report Resource Website 5000+ mentions |
FastTree (RRID:SCR_015501) | software resource, source code | Source code that infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. It uses the Jukes-Cantor or generalized time-reversible (GTR) models of nucleotide evolution and the JTT, WAG, or LG models of amino acid evolution. | phylogenetic tree, phylogenetic tree creation, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is related to: VeryFastTree |
PMID:19377059 DOI:10.1371/journal.pone.0009490 |
biotools:fasttree, OMICS_14703 | https://bio.tools/fasttree, https://sources.debian.org/src/fasttree/ | SCR_015501 | 2026-08-03 09:35:59 | 5774 | ||||||||
|
lme4 Resource Report Resource Website 100+ mentions |
lme4 (RRID:SCR_015654) | software resource, source code | Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue." | linear mixed-effects model, s4 class, eigen c++ library, r package, r, bio.tools |
is listed by: CRAN is listed by: bio.tools is listed by: Debian works with: R package: lmerTest |
Free, Available for download | biotools:lme4 | https://cran.r-project.org/package=lme4, https://github.com/lme4/lme4/, https://bio.tools/lme4 | SCR_015654 | lme4, lme4.0, lme4: Linear Mixed-Effects Models using 'Eigen' and S4, lme4: Linear Mixed-Effects Models, R package: lme4 | 2026-08-03 09:36:03 | 327 | |||||||
|
EGSEA Resource Report Resource Website 50+ mentions |
EGSEA (RRID:SCR_015036) | software toolkit, software resource, source code | Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets. | gene set, rna sequencing, analysis method, r package, bio.tools |
is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
Victorian State Government Operational Infrastructure Support ; Australian Government NHMRC IRIISS ; NHMRC GNT1050661; NHMRC GNT1045936; NHMRC GNT1057854; NHMRC GNT1104924 |
PMID:27694195 | Free, Available for download | biotools:egsea | https://bio.tools/egsea | SCR_015036 | Ensemble of Gene Set Enrichment Analyses (EGSEA), Ensemble of Gene Set Enrichment Analyses | 2026-08-03 09:35:43 | 62 | |||||
|
Sequence Search and Alignment by Hashing Algorithm Resource Report Resource Website 1+ mentions |
Sequence Search and Alignment by Hashing Algorithm (RRID:SCR_000544) | SSAHA2 | software resource, source code | A program designed for the efficient mapping of sequence reads onto genomic references. The software is capable of reading most sequencing platforms and giving a range of outputs are supported. | sequence, genomic, analysis, search, alignment, algorithm, mapping, bio.tools |
is listed by: OMICtools is listed by: bio.tools is related to: SMALT has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:11591649 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ssaha2, OMICS_00690, nlx_93831 | https://bio.tools/ssaha2 | SCR_000544 | ssaha2, ssaha, Sequence Search and Alignment by Hashing Algorithm | 2026-08-03 09:31:04 | 6 | |||||
|
DecGPU Resource Report Resource Website 1+ mentions |
DecGPU (RRID:SCR_000585) | software resource | Software tool as parallel and distributed error correction algorithm for high-throughput short reads using CUDA and MPI parallel programming models. | k-mer based corrector, k-mer spectrum, illumina short read, multistage workflow, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21447171 | Free, Available for download, Freely available | biotools:decgpu, OMICS_01101, SCR_011850, OMICS_01060 | http://musket.sourceforge.net/homepage.htm#latest, https://bio.tools/decgpu | SCR_000585 | Distributed short read Error Correction on GPUs | 2026-08-03 09:31:06 | 5 | ||||||
|
RNAplex Resource Report Resource Website 10+ mentions |
RNAplex (RRID:SCR_002763) | RNAplex | software resource, source code | Software tool to rapidly search for short interactions between two long RNAs. | interaction, rna, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Leipzig; Saxony; Germany |
PMID:21593134 PMID:18434344 |
Free, Freely available, Available for download | rid_000107, biotools:rnaplex | https://bio.tools/rnaplex | SCR_002763 | 2026-08-03 09:31:49 | 37 | ||||||
|
BamView Resource Report Resource Website 10+ mentions |
BamView (RRID:SCR_004207) | BamView | software resource, source code | A free interactive display of read alignments in BAM data files that can be launched with Java Web Start or downloaded. This interactive Java application for visualizing the large amounts of data stored for sequence reads which are aligned against a reference genome sequence can be used in a number of contexts including SNP calling and structural annotation. It has been integrated into Artemis so that the reads can be viewed in the context of the nucleotide sequence and genomic features. The source code is available as part of the Artemis code which can be downloaded from GitHub. | bam, next-generation sequencing, java, snp calling, structural annotation, macosx, unix, windows, visualize, analyze, sequence read, reference sequence, single nucleotide polymorphism, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:22253280 PMID:20071372 |
GNU General Public License | biotools:bamview, OMICS_00878, nlx_22933 | https://bio.tools/bamview | SCR_004207 | 2026-08-03 09:32:23 | 21 | ||||||
|
Genomedata Resource Report Resource Website |
Genomedata (RRID:SCR_004544) | Genomedata | software resource, source code | A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems. | genome, data, format, linux, mac, functional genomics, function, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: bio.tools is listed by: Debian has parent organization: University of Washington; Seattle; USA |
PMID:20435580 | GNU General Public License | nlx_53677, biotools:genomedata, OMICS_02148 | https://bio.tools/genomedata | SCR_004544 | 2026-08-03 09:32:28 | 0 | ||||||
|
Strelka2 Resource Report Resource Website 100+ mentions |
Strelka2 (RRID:SCR_005109) | software resource, source code | Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller. | single nucleotide variant, indel, somatic snv, next-generation sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Illumina |
Cancer, Tumor, Normal | PMID:22581179 PMID:30013048 |
Free, Available for download, Freely available | biotools:strelka | https://bio.tools/strelka, https://sources.debian.org/src/strelka/ | http://bioinformatics.oxfordjournals.org/content/early/2012/05/10/bioinformatics.bts271.full.pdf | SCR_005109 | Strelka | 2026-08-03 09:32:47 | 261 | ||||
|
ALCHEMY Resource Report Resource Website 1+ mentions |
ALCHEMY (RRID:SCR_005761) | ALCHEMY | software resource, source code | ALCHEMY is a genotype calling algorithm for Affymetrix and Illumina products which is not based on clustering methods. Features include explicit handling of reduced heterozygosity due to inbreeding and accurate results with small sample sizes. ALCHEMY is a method for automated calling of diploid genotypes from raw intensity data produced by various high-throughput multiplexed SNP genotyping methods. It has been developed for and tested on Affymetrix GeneChip Arrays, Illumina GoldenGate, and Illumina Infinium based assays. Primary motivations for ALCHEMY''s development was the lack of available genotype calling methods which can perform well in the absence of heterozygous samples (due to panels of inbred lines being genotyped) or provide accurate calls with small sample batches. ALCHEMY differs from other genotype calling methods in that genotype inference is based on a parametric Bayesian model of the raw intensity data rather than a generalized clustering approach and the model incorporates population genetic principles such as Hardy-Weinberg equilibrium adjusted for inbreeding levels. ALCHEMY can simultaneously estimate individual sample inbreeding coefficients from the data and use them to improve statistical inference of diploid genotypes at individual SNPs. The main documentation for ALCHEMY is maintained on the sourceforge-hosted MediaWiki system. Features * Population genetic model based SNP genotype calling * Simultaneous estimation of per-sample inbreeding coefficients, allele frequencies, and genotypes * Bayesian model provides posterior probabilities of genotype correctness as quality measures * Growing number of scripts and supporting programs for validation of genotypes against control data and output reformating needs * Multithreaded program for parallel execution on multi-CPU/core systems * Non-clustering based methods can handle small sample sets for empirical optimization of sample preparation techniques and accurate calling of SNPs missing genotype classes ALCHEMY is written in C and developed on the GNU/Linux platform. It should compile on any current GNU/Linux distribution with the development packages for the GNU Scientific Library (gsl) and other development packages for standard system libraries. It may also compile and run on Mac OS X if gsl is installed. | diploid, genotype, snp, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Cornell University; New York; USA |
NSF 0606461 | PMID:20926420 | GNU General Public License | biotools:alchemy, nlx_149227 | https://bio.tools/alchemy | SCR_005761 | ALCHEMY - An automated population genetic model driven SNP genotype calling method | 2026-08-03 09:32:55 | 5 | ||||
|
BAIT Resource Report Resource Website 1+ mentions |
BAIT (RRID:SCR_000511) | BAIT | data processing software, data analysis software, software resource, software application, data visualization software | Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data. | create strand inheritance plots, strand-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24028793 | Free, Available for download, Freely available | biotools:bait, OMICS_01531 | https://bio.tools/bait | SCR_000511 | BAIT - Software to help analyse Strand-Seq data | 2026-08-04 09:40:09 | 1 | |||||
|
Human Disease Ontology Resource Report Resource Website 1+ mentions |
Human Disease Ontology (RRID:SCR_000476) | DO | ontology, database, data or information resource, controlled vocabulary | Comprehensive hierarchical controlled vocabulary for human disease representation.Open source ontology for integration of biomedical data associated with human disease. Disease Ontology database represents comprehensive knowledge base of inherited, developmental and acquired human diseases. | obo, pathological, organismal, cellular, disease, biomedical, health, neurologic disease, neurological disorder, phenotype, bio.tools, |
is used by: DOAF is listed by: BioPortal is listed by: OBO is listed by: bio.tools is listed by: Debian is related to: PharmGKB Ontology is related to: GWASdb is related to: NUgene Project is related to: FunDO is related to: Neurocarta has parent organization: University of Maryland School of Medicine; Maryland; USA |
NHGRI U24 HG012557 | PMID:22080554 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-35926, nlx_157432, SCR_003491, biotools:disease_ontology | http://disease-ontology.org/, https://bio.tools/disease_ontology, http://purl.obolibrary.org/obo/doid.obo, | http://do-wiki.nubic.northwestern.edu/index.php/Main_Page | SCR_000476 | Human Disease Ontology Knowledgebase, Disease Ontology | 2026-08-04 09:40:08 | 5 | |||
|
MPscan Resource Report Resource Website |
MPscan (RRID:SCR_000587) | MPscan | data access protocol, software resource, web service | Web tool for index free mapping of multiple short reads on a genome. | linux, macos, next-generation sequencing, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: ATGC: Montpellier bioinformatics platform |
Free, Available for download, Freely available | biotools:mpscan, OMICS_00670 | https://bio.tools/mpscan | SCR_000587 | MPscan: index free mapping of multiple short reads on a genome | 2026-08-04 09:40:10 | 0 | ||||||
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POPBAM Resource Report Resource Website |
POPBAM (RRID:SCR_000464) | POPBAM | data processing software, software application, software resource, data analysis software | A tool to perform evolutionary or population-based analyses of next-generation sequencing data. POPBAM takes a BAM file as its input and can compute many widely used evolutionary genetics measures in sliding windows across a genome. | next-generation sequencing, evolution, population, bam, genome, evolutionary genetics, c++, short read, sequence alignment, sliding window, command-line, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: University of Rochester; New York; USA |
PMID:24027417 | Free, Available for download, Freely available | biotools:popbam, OMICS_01559 | https://bio.tools/popbam | http://popbam.sourceforge.net/ | SCR_000464 | 2026-08-04 09:40:08 | 0 | |||||
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Skylign Resource Report Resource Website 10+ mentions |
Skylign (RRID:SCR_001176) | Skylign | data analysis service, analysis service resource, software resource, production service resource, service resource | A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position. | sequence alignment, profile, logo, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research |
PMID:24410852 | Creative Commons Attribution License, v3 Unported | biotools:skylign, OMICS_02182 | https://bio.tools/skylign | SCR_001176 | Skylign - Interactive logos for alignments and profile HMMs | 2026-08-04 09:40:20 | 13 | |||||
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sim4cc Resource Report Resource Website |
sim4cc (RRID:SCR_001204) | data processing software, alignment software, software resource, software application, image analysis software | Software tool as cross species spliced alignment program.Heuristic sequence alignment tool for comparing cDNA sequence with genomic sequence containing homolog of gene in another species. | Cross species spliced alignment, unix, sequence alignment, cdna sequence, genomic sequence, homolog, gene, splice, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Johns Hopkins University; Maryland; USA |
NSF CLS20163A; Sloan Research Fellowship ; NLM R01 LM006845 |
PMID:19429899 | Free, Available for download, Freely available | biotools:sim4cc, OMICS_02145 | https://bio.tools/sim4cc | SCR_001204 | 2026-08-04 09:40:20 | 0 | ||||||
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bsseq Resource Report Resource Website 1+ mentions |
bsseq (RRID:SCR_001072) | data processing software, data analysis software, software resource, sequence analysis software, software application | R package with tools for analyzing and visualizing bisulfite sequencing data. | bisulfite sequencing, analyze, r, sequence analysis software, data analysis software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01847, biotools:bsseq | https://bio.tools/bsseq | SCR_001072 | bsseq - Analyze manage and store bisulfite sequencing data | 2026-08-04 09:40:18 | 8 | |||||||
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SplitSeek Resource Report Resource Website 1+ mentions |
SplitSeek (RRID:SCR_001012) | data processing software, data analysis software, software resource, sequence analysis software, software application | THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data. | bioinformatics alignment, sequence analysis software, de novo, prediction, rna seq, rna, splice junction, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20236510 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:splitseek, OMICS_01253 | https://bio.tools/splitseek | http://www.uppmax.uu.se/software/splitseek | SCR_001012 | 2026-08-04 09:40:16 | 1 |
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