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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Google Scholar Resource Report Resource Website 10000+ mentions |
Google Scholar (RRID:SCR_008878) | Google Scholar | data or information resource, database | Google Scholar provides a simple way to broadly search for scholarly literature. From one place, you can search across many disciplines and sources: articles, theses, books, abstracts and court opinions, from academic publishers, professional societies, online repositories, universities and other web sites. Google Scholar helps you find relevant work across the world of scholarly research. Features of Google Scholar * Search diverse sources from one convenient place * Find articles, theses, books, abstracts or court opinions * Locate the complete document through your library or on the web * Learn about key scholarly literature in any area of research How are documents ranked? Google Scholar aims to rank documents the way researchers do, weighing the full text of each document, where it was published, who it was written by, as well as how often and how recently it has been cited in other scholarly literature. * Publishers - Include your publications in Google Scholar * Librarians - Help patrons discover your library''s resources | literature |
is used by: Writefull is listed by: SoftCite is parent organization of: Google Scholar Blog |
nlx_151304 | SCR_008878 | 2026-09-19 12:57:20 | 43739 | |||||||||
|
T-Coffee Resource Report Resource Website 1000+ mentions |
T-Coffee (RRID:SCR_011818) | T-Coffee | analysis service resource, data analysis service, production service resource, service resource | A multiple sequence alignment server which can align Protein, DNA and RNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:10964570 DOI:10.1006/jmbi.2000.4042 |
biotools:tcoffee, OMICS_00989 | https://bio.tools/tcoffee, https://sources.debian.org/src/t-coffee/ | SCR_011818 | T-Coffee: Aligns DNA RNA or Proteins using the default T-Coffee | 2026-09-19 12:57:25 | 1157 | ||||||
|
ProbCons Resource Report Resource Website 100+ mentions |
ProbCons (RRID:SCR_011813) | ProbCons | analysis service resource, data analysis service, production service resource, service resource | Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Stanford University; Stanford; California |
PMID:15687296 DOI:10.1101/gr.2821705 |
OMICS_00986, biotools:probcons | https://bio.tools/probcons, https://sources.debian.org/src/probcons/ | SCR_011813 | ProbCons: Probabilistic Consistency-based Multiple Alignment of Amino Acid Sequences | 2026-09-19 12:57:25 | 109 | ||||||
|
GeneVenn Resource Report Resource Website 100+ mentions |
GeneVenn (RRID:SCR_012117) | analysis service resource, data analysis service, production service resource, service resource | A web application creating Venn diagrams from two or three gene lists. | web app |
is listed by: OMICtools is listed by: SoftCite has parent organization: SourceForge |
PMID:17597932 | OMICS_05568 | SCR_012117 | 2026-09-19 12:57:26 | 107 | |||||||||
|
TBLASTN Resource Report Resource Website 5000+ mentions |
TBLASTN (RRID:SCR_011822) | TBLASTN | analysis service resource, data analysis service, production service resource, service resource | Tool to search translated nucleotide databases using a protein query. | protein |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
OMICS_00999 | SCR_011822 | Translated BLAST: tblastn | 2026-09-19 12:57:25 | 5696 | ||||||||
|
FGENESH Resource Report Resource Website 100+ mentions |
FGENESH (RRID:SCR_011928) | FGENESH | analysis service resource, data analysis service, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:fgenesh, OMICS_01483 | https://bio.tools/fgenesh | SCR_011928 | 2026-09-19 12:57:25 | 330 | |||||||
|
BaCelLo Resource Report Resource Website 10+ mentions |
BaCelLo (RRID:SCR_011965) | BaCelLo | analysis service resource, data analysis service, production service resource, service resource | A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable. | protein, data set, proteome |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bologna; Bologna; Italy |
PMID:16873501 | OMICS_01616 | SCR_011965 | 2026-09-19 12:57:26 | 46 | ||||||||
|
Ensembl Genome Browser Resource Report Resource Website 1000+ mentions |
Ensembl Genome Browser (RRID:SCR_013367) | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17,2022. Genome databases for vertebrates and other eukaryotic species. Analysis and annotation maintained on current data.Distribution of analysis to other bioinformatics laboratories. Ensembl concentrates on vertebrate genomes, but other groups have adapted system for use with plant and fungal genomes (see Powered by Ensembl list on website). |
is listed by: SoftCite has parent organization: Ensembl |
European Bioinformatics Institute ; Wellcome Trust Sanger Institute |
THIS RESOURCE IS NO LONGER IN SERVICE. | nif-0000-30518 | http://uswest.ensembl.org/index.html | SCR_013367 | 2026-09-19 12:57:30 | 1199 | ||||||||
|
SciPy Resource Report Resource Website 10000+ mentions |
SciPy (RRID:SCR_008058) | software application, software resource | A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console. | python, software, open source |
uses: Python Programming Language is used by: PyDSTool is used by: Elephant is used by: Stimfit is used by: Sklearn is listed by: SoftCite is related to: IPython is related to: NumPy is related to: IPython Notebook is related to: MNE software is related to: DE-Sim is required by: TomoMiner is required by: Short Read Sequence Typing for Bacterial Pathogens |
Public, Free | nif-0000-10422 | SCR_008058 | SciPy, Scientific Tools for Python | 2026-09-19 12:57:55 | 16188 | ||||||||
|
Statistical Analysis System Resource Report Resource Website 5000+ mentions |
Statistical Analysis System (RRID:SCR_008567) | SAS | data analytics software, data management software, software application, software resource | Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS. | Explore, analyze, visualize, data, standardized, management, statistics | is listed by: SoftCite | Restircted | nif-0000-31484 | https://www.sas.com/en_us/software/platform.html, https://www.sas.com/en_us/software/sas9.html | SCR_008567 | Statistical Analysis System, SAS Intelligence Platform, SAS 9.3, SAS 9.4 | 2026-09-19 12:57:55 | 7485 | ||||||
|
GENIE Resource Report Resource Website 100+ mentions |
GENIE (RRID:SCR_009197) | GENIE | software application, software resource | Software application that performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, java 1.6, web-based |
is listed by: Genetic Analysis Software is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154344 | http://bioinformatics.med.utah.edu/Genie/index.html | SCR_009197 | PEDGENIE, HAPMC | 2026-09-19 12:58:01 | 361 | ||||||
|
PROFILER Resource Report Resource Website 1000+ mentions |
PROFILER (RRID:SCR_009339) | PROFILER | software application, software resource | A flexible software tool to generate the probability distribution of joint multilocus genotypes defined by sets of individuals within the pedigree and sets of markers within the framework map. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, linux, unix, solaris |
is listed by: Genetic Analysis Software is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154552 | SCR_009339 | 2026-09-19 12:58:04 | 1295 | ||||||||
|
Web of Science Resource Report Resource Website 10+ mentions |
Web of Science (RRID:SCR_022706) | data or information resource, database | Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database. | Clarivate, publisher independent, global citation database, bibliographic citations of multidisciplinary areas, various journals | is listed by: SoftCite | Free | SCR_022706 | Web of Knowledge | 2026-09-19 12:57:39 | 24 | |||||||||
|
CASAVA Resource Report Resource Website 1000+ mentions |
CASAVA (RRID:SCR_001802) | CASAVA | software application, software resource | Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting | gene, genetic, genomic, linux |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite |
Free, Available for download, Freely available | nlx_154257, OMICS_01123 | http://www.illumina.com/software/genome_analyzer_software.ilmn | SCR_001802 | Consensus Assessment of Sequence And VAriation | 2026-09-19 12:57:44 | 1960 | ||||||
|
RNALocate Resource Report Resource Website 10+ mentions |
RNALocate (RRID:SCR_024418) | data access protocol, software resource, web service | Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation. | RNA subcellular localizations analysis, | is listed by: SoftCite | Scientific Research Fund of Heilongjiang Provincial Education Department ; National Key Research and Development Project of China ; National Natural Science Foundation of China ; Paul K. and Diane Shumaker Endowment Fund at University of Missouri ; Guangdong Basic and Applied Basic Research Foundation |
PMID:27543076 PMID:34551440 |
Free, Freely available | http://www.rna-society.org/rnalocate/, http://www.rnalocate.org/ | SCR_024418 | RNALOCATE, RNALocate v2.0 | 2026-09-19 12:55:43 | 24 | ||||||
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SRAMP Resource Report Resource Website 100+ mentions |
SRAMP (RRID:SCR_024500) | simulation software, software application, software resource | Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. | mammalian m(6)A site predictor, sequence derived features based predictor, | is listed by: SoftCite | PMID:26896799 | Free, Available for download, Freely available | SCR_024500 | Sequence-based Rna Adenosine Methylation site Predictor | 2026-09-19 12:55:44 | 452 | ||||||||
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RNAfold Resource Report Resource Website 100+ mentions |
RNAfold (RRID:SCR_024427) | data access protocol, software resource, web service | Web server predict secondary structures of single stranded RNA or DNA sequences. | predict secondary structures, single stranded RNA, DNA sequences, | is listed by: SoftCite | Free, Freely available | SCR_024427 | 2026-09-19 12:55:44 | 100 | ||||||||||
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Nano Measurer Resource Report Resource Website 1+ mentions |
Nano Measurer (RRID:SCR_024493) | data analysis software, data processing software, software application, software resource | Software tool to process micrograph images for particle size. | process micrograph images, images for particle size, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024493 | 2026-09-19 12:55:44 | 9 | ||||||||||
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ToposPro Resource Report Resource Website 10+ mentions |
ToposPro (RRID:SCR_024496) | data analysis software, data processing software, software application, software resource | Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters. | geometrical and topological properties analysis, crystals, networks, tilings, periodic structures analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024496 | 2026-09-19 12:55:44 | 18 | ||||||||||
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Stem Resource Report Resource Website 1+ mentions |
Stem (RRID:SCR_024499) | data analysis software, data processing software, software application, software resource | Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology. | short time series gene expression data analysis, clustering, comparing, visualizing, short time series gene expression data, microarray experiments data, identify temporal expression profiles identify genes associated with expression profiles, compare behavior of genes across multiple conditions, | is listed by: SoftCite | PMID:16597342 | Free, Available for download, Freely available | SCR_024499 | Short Time-series Expression Miner | 2026-09-19 12:55:44 | 6 |
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