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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Assisted Model Building with Energy Refinement (AMBER) Resource Report Resource Website 1000+ mentions |
Assisted Model Building with Energy Refinement (AMBER) (RRID:SCR_014230) | AMBER | simulation software, software application, software resource, standalone software | Software package of molecular simulation programs. It is distributed into AmberTools15 and Amber14. AmberTools15 is a software package which can carry out complete molecular dynamics simulations with either explicit water or generalized Born solvent models. It is distributed in source code format and must be compiled in order to be used. Amber14 builds on AmberTools15 by adding the pmemd program, which provides better performance on multiple CPUs and dramatic speed improvements on GPUs compared to sander (molecular dynamics). GPU info, manuals, and tutorials are available on the website. | molecular simulation, simulation software, software package, molecular dynamics, pmemed, sander, bio.tools |
is listed by: bio.tools is listed by: Debian |
Acknowledgement requested | biotools:amber | https://bio.tools/amber | SCR_014230 | Assisted Model Building with Energy Refinement | 2026-09-12 01:01:02 | 4081 | ||||||
|
PALEOMIX Resource Report Resource Website 50+ mentions |
PALEOMIX (RRID:SCR_015057) | data processing software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software toolkit for the processing of ancient and modern HTS data. PALEOMIX also aids in metagenomic analysis of the extracts from the HTS processing. | hts data, high-throughput sequencing, ancient dna, adna, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:24722405 DOI:10.1038/nprot.2014.063 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:paleomix, OMICS_03749 | https://bio.tools/paleomix, https://sources.debian.org/src/paleomix/ | SCR_015057 | 2026-09-12 01:01:03 | 66 | |||||||
|
docker4seq Resource Report Resource Website 1+ mentions |
docker4seq (RRID:SCR_017006) | data processing software, software application, software resource | Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers. | next, generation, sequencing, computing, application, read, mapping, count, docker, container, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
Free, Available for download, Freely available | biotools:docker4seq | https://kendomaniac.github.io/docker4seq/index.html, https://bio.tools/docker4seq | SCR_017006 | 2026-09-12 01:01:05 | 6 | ||||||||
|
NeLS Resource Report Resource Website 1+ mentions |
NeLS (RRID:SCR_016301) | NeLS | data or information resource, organization portal, portal | Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project. | genomic, data, analyze, store, share, archive, electronic, infrastructure, administration, Norway, bio.tools |
is listed by: bio.tools is listed by: Debian |
Research Council of Norway | Free, Freely available | biotools:nels | https://bio.tools/nels, https://github.com/elixir-no-nels/nels-core, https://bio.tools/nels | SCR_016301 | Norwegian e-Infrastructure for Life Sciences | 2026-09-12 01:01:04 | 3 | |||||
|
GeSeq Resource Report Resource Website 500+ mentions |
GeSeq (RRID:SCR_017336) | data processing software, service resource, software application, software resource | Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes. | rapid, accurate, annotation, organelle, genome, chloroplast, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
German Science Foundation ; Human Frontier Science Program ; Max Planck Society |
PMID:28486635 | Free, Freely available | biotools:geseq | https://bio.tools/geseq | SCR_017336 | 2026-09-12 01:01:05 | 535 | ||||||
|
ProCon - PROteomics CONversion Resource Report Resource Website 1+ mentions |
ProCon - PROteomics CONversion (RRID:SCR_016363) | ProCon | data processing software, software application, software resource | Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. | data, proteomics, conversion, file, laboratory, information, management, system, database, standard, format, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Ruhr University Bochum; North Rhine-Westphalia; Germany |
European Union Projects ProDac ; European Union Projects ProteomeXchange ; the German Federal Ministry of Education and Research BMBF |
PMID:26182917 | Free, Available for download, Freely available | biotools:procon | https://bio.tools/procon | SCR_016363 | PROteomics CONversion | 2026-09-12 01:01:04 | 1 | ||||
|
ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | data processing software, software application, software resource | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch, https://bio.tools/scaffmatch | SCR_017025 | 2026-09-12 01:01:05 | 1 | ||||||
|
STRUCTURE Resource Report Resource Website 1000+ mentions |
STRUCTURE (RRID:SCR_017637) | software resource, software toolkit | Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms. | Multi locus genotype data, investigate population structure, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: STRAT has parent organization: Stanford University; Stanford; California works with: Structure Harvester |
PMID:21564903 PMID:18784791 PMID:12930761 PMID:10835412 |
Free, Available for download, Freely available | SCR_021634, nlx_154662, SCR_002151, biotools:structure | https://bio.tools/structure, http://pritch.bsd.uchicago.edu/structure.html, | SCR_017637 | structure, Structure | 2026-09-12 01:01:06 | 4177 | ||||||
|
Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | data processing software, software application, software resource | Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies. | Assembly, de novo, long, uncorrected, read, raw, contig, consensus, step, data, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
A*STAR ; Singapore ; Croatian Academy of Sciences and Arts ; Croatian Science Foundation |
DOI:10.1101/068122 | Free, Available for download, Freely available | OMICS_25714, biotools:Racon, BioTools:Racon | https://bio.tools/Racon, https://sources.debian.org/src/racon/ | SCR_017642 | 2026-09-12 01:01:06 | 177 | ||||||
|
seq-annot Resource Report Resource Website 1+ mentions |
seq-annot (RRID:SCR_018731) | software application, software resource, software toolkit, standalone software | Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes. | Annotating, counting, comparison, genomic feature, genome, metagenome, metagenomics, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:seq-annot | https://bio.tools/seq-annot | SCR_018731 | 2026-09-12 01:01:07 | 1 | ||||||||
|
TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | data processing software, software application, software resource, standalone software | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder, https://sources.debian.org/src/transdecoder/, https://github.com/TransDecoder/TransDecoder/wiki | SCR_017647 | , Find Coding Regions Within Transcripts | 2026-09-12 01:01:06 | 1572 | |||||||
|
QuPath Resource Report Resource Website 1000+ mentions |
QuPath (RRID:SCR_018257) | data processing software, image analysis software, software application, software resource | Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images. | Digital pathology, image analysis, whole slide image, batch processing, tissue image, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Queens University Belfast; Ireland; United Kingdom |
Cancer Research UK Accelerator ; Experimental Cancer Medicine Centre Network ; Friends of the Cancer Centre ; Invest Northern Ireland ; Sean Crummey Memorial Fund ; Tom Simms Memorial Fund |
PMID:29203879 | Free, Available for download, Freely available | biotools:qupath | https://bio.tools/qupath | SCR_018257 | 2026-09-12 01:01:07 | 2084 | ||||||
|
FlowCal Resource Report Resource Website 1+ mentions |
FlowCal (RRID:SCR_018140) | data processing software, software application, software resource | Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots. | Converting flow cytometry data, arbitrary unit, calibrated unit, data gating, statistic, plot, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NDSEG Fellowship ; NIAID R21 AI115014; NSF Graduate Research Fellowship DGE 0940902; NSF EFRI 1137266; NSF MCB 1244135; Office of Naval Research MURI N000141310074; Office of Naval Research YIP N000141410487; Welch Foundation |
PMID:27110723 | Free, Available for download, Freely available | biotools:flowcal | https://bio.tools/flowcal | SCR_018140 | Python Flow Cytometry Calibration Library | 2026-09-12 01:01:07 | 6 | |||||
|
halSynteny Resource Report Resource Website 1+ mentions |
halSynteny (RRID:SCR_018127) | data processing software, software application, software resource | Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment. | Conserved synteny, block construction method, genome alignment, DAG based reconstruction, synteny block, chromosome, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:halSynteny | https://bio.tools/halSynteny | SCR_018127 | Hierarchical Alignment Format Synteny | 2026-09-12 01:01:06 | 4 | |||||||
|
CiLiQuant Resource Report Resource Website |
CiLiQuant (RRID:SCR_019319) | data processing software, software application, software resource | Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance. | RNA, splicing, circular origin, separate junction reads, circular transcript abundance, linear transcript abundance, compare, bio.tools |
is listed by: bio.tools is listed by: Debian |
European Union's Horizon 2020 ; FWO ; Kom Op Tegen Kanker (Stand Up To Cancer) ; Special Research Fund UGent ; Stichting Tegen Kanker |
Free, Available for download, Freely available | biotools:ciliquant | https://bio.tools/ciliquant | SCR_019319 | 2026-09-12 01:01:08 | 0 | |||||||
|
fgsea Resource Report Resource Website 100+ mentions |
fgsea (RRID:SCR_020938) | data analysis software, data processing software, software application, software resource | Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. | Gene set enrichment analysis, preranked gene set, multiple hypothesis correction, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
DOI:10.1101/060012 | Free, Available for download, Freely available | biotools:fgsea | https://github.com/ctlab/fgsea/, https://bio.tools/fgsea | SCR_020938 | fast gene set enrichment analysis, Fast Gene Set Enrichment Analysis, FGSEA | 2026-09-12 12:59:48 | 237 | ||||||
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Bs-Seeker2 Resource Report Resource Website 1+ mentions |
Bs-Seeker2 (RRID:SCR_020948) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels. | Versatile aligning pipeline, bisulfite sequencing data, mapping bisulfite sequencing data, generating DNA methylomes, DNA methylation level, reads mapping, Reduced Represented Bisulfite Sequencing library, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: BS Seeker has parent organization: University of California at Los Angeles; California; USA |
China Scholarship Council ; Institute of Genomics and Proteomics at UCLA ; NBRPC 2012CB316503 |
PMID:24206606 | Free, Available for download, Freely available | biotools:bs-seeker2 | http://pellegrini.mcdb.ucla.edu/BS_Seeker2/, https://bio.tools/bs-seeker2 | SCR_020948 | Bisulfite Sequencing Seeker2, BS Seeker2 | 2026-09-12 12:59:48 | 2 | |||||
|
Omics Data Paper Generator Resource Report Resource Website 1+ mentions |
Omics Data Paper Generator (RRID:SCR_019809) | data access protocol, data processing software, documentation generation software, software application, software development tool, software resource, web service, workflow software | Software package for streamlined import of omics metadata from European Nucleotide Archive into OMICS Data Paper manuscript. Omics Data Paper R Shiny app demonstrates workflow for automatic import of ENA genomic metadata into omics data paper manuscript. Streamlined conversion of metadata into manuscript facilitates authoring of omics data papers, which allow omics dataset creators to receive credit for their work and to improve description and visibility of their datasets. | Workflow, genomics, omics, FAIR data, data paper, G Power, European Nucleotide Archive, genomic metadata, omics data paper manuscript, streamlined conversion, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Shiny |
Horizon 2020 764840 | Free, Available for download, Freely available | biotools:omics-data-paper-shinyapp-golem | https://mdmtrv.shinyapps.io/Omics_data_paper/, https://bio.tools/omics-data-paper-shinyapp-golem | SCR_019809 | omicsdatapaper | 2026-09-12 12:59:23 | 1 | ||||||
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circlize Resource Report Resource Website 1000+ mentions |
circlize (RRID:SCR_002141) | software application, software resource, standalone software | Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style. | circular visualization, draw statistical graphics, circular style graphics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24930139 | Free, Available for download, Freely available | OMICS_04658, biotools:circlize | https://github.com/jokergoo/circlize, https://bio.tools/circlize | SCR_002141 | circlize: Circular Visualization in R | 2026-09-12 01:02:27 | 1289 | ||||||
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GERMLINE Resource Report Resource Website 100+ mentions |
GERMLINE (RRID:SCR_001720) | GERMLINE | software application, software resource | Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, c++, linux, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Columbia University; New York; USA |
PMID:18971310 | Free, Available for download, Freely available | biotools:germline, OMICS_00202, nlx_154080 | https://bio.tools/germline | http://www1.cs.columbia.edu/~gusev/germline/ | SCR_001720 | 2026-09-12 01:02:26 | 451 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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