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  description: OpenProteo is the open-source Rust stack for proteomics raw-file access.
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  description: OpenWRaw is a standalone, cross-platform reader for Waters MassLynx
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  description: OpenTFRaw is a standalone, cross-platform reader for Thermo Fisher
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  topic:
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    uri: http://edamontology.org/topic_3332
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2023-09-05T09:39:45.613658Z'
  biotoolsCURIE: biotools:squarna
  biotoolsID: squarna
  collectionID:
  - 3D-BioInfo-Nucleic-Acid
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: efbaulin@gmail.com
    fundrefid: null
    gridid: null
    name: Eugene F Baulin
    note: https://imol.institute/leaders/baulin-group/
    orcidid: https://orcid.org/0000-0003-4694-9783
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Support
    url: https://scholar.google.com/citations?user=sjfDaUwAAAAJ&hl=en
  description: SQUARNA is a tool for RNA secondary structure prediction. It can take
    a single RNA sequence or an alignment of sequences as input. SQUARNA handles pseudoknots
    and can predict alternative structures. SQUARNA allows structural restraints and
    chemical probing data as additional input and is available at https://github.com/febos/SQUARNA
    and https://larnal.imol.institute/.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/febos/SQUARNA/blob/main/README.md
  - note: pip install SQUARNA
    type:
    - Installation instructions
    url: https://pypi.org/project/SQUARNA/
  download:
  - note: null
    type: Downloads page
    url: https://doi.org/10.5281/zenodo.8292325
    version: '3.22'
  - note: pip install SQUARNA
    type: Software package
    url: https://pypi.org/project/SQUARNA/
    version: '3.22'
  editPermission:
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  function:
  - cmd: SQUARNA i=inputfile [OPTIONS]
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
    - data:
        term: Structural profile
        uri: http://edamontology.org/data_0889
      format: []
    note: Input can be a single or several RNA sequences or an alignment of RNA sequences
      along with structural restraints and/or chemical probing data on base reactivities
    operation:
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    output:
    - data:
        term: RNA secondary structure
        uri: http://edamontology.org/data_0880
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: https://github.com/febos/SQUARNA
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-07-03T09:33:38.948762Z'
  license: Apache-2.0
  link:
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/febos/SQUARNA
  - note: PyPi repository page
    type:
    - Software catalogue
    url: https://pypi.org/project/SQUARNA/
  - note: Web server
    type:
    - Service
    url: https://larnal.imol.institute/
  maturity: Emerging
  name: SQUARNA
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: febos
  publication:
  - doi: 10.64898/2026.06.30.735492
    metadata: null
    note: biorxiv preprint
    pmcid: null
    pmid: null
    type:
    - Primary
    version: '3.22'
  relation: []
  toolType:
  - Command-line tool
  - Library
  - Web application
  - Script
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: RNA
    uri: http://edamontology.org/topic_0099
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  validated: 0
  version:
  - '3.22'
- accessibility: Open access
  additionDate: '2026-06-18T00:24:30.316906Z'
  biotoolsCURIE: biotools:mircounts
  biotoolsID: mircounts
  collectionID:
  - Galaxy Tools
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: "Generates pre-miRNA and mature miRNA count tables from read alignments\
    \ to\n  pre-miRNA sequences and a gff file, both downloaded from mirBase. Produces\
    \ also read coverage plots of pre-miRNAs."
  documentation: []
  download: []
  editPermission:
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Read mapping
      uri: http://edamontology.org/operation_3198
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output: []
  homepage: https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts
  homepage_status: 0
  language:
  - Shell
  - Python
  - R
  lastUpdate: '2026-07-02T09:12:34.528282Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ARTbio/tools-artbio/tree/main/tools/mircounts
  - note: null
    type:
    - Other
    url: http://artbio.fr
  maturity: Mature
  name: miRcounts
  operatingSystem: []
  otherID: []
  owner: VKasalica
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 0
  version: []
- accessibility: null
  additionDate: '2015-01-22T11:13:24Z'
  biotoolsCURIE: biotools:clustvis
  biotoolsID: clustvis
  collectionID:
  - Elixir-EE
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: ELIXIR-EE
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: tauno.metsalu@ut.ee
    fundrefid: null
    gridid: null
    name: Tauno Metsalu
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: biit.support@ut.ee
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Web tool which allows users to upload their own data and easily create
    Principal Component Analysis (PCA) plots and heatmaps. Data can be uploaded as
    a file or by copy-pasteing it to the text box.
  documentation:
  - note: null
    type:
    - General
    url: https://biit.cs.ut.ee/clustvis/
  download:
  - note: Docker image
    type: Container file
    url: https://hub.docker.com/r/taunometsalu/clustvis/
    version: null
  editPermission:
    authors:
    - may.kay
    type: group
  elixirCommunity: []
  elixirNode:
  - Estonia
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Processed microarray data
        uri: http://edamontology.org/data_3111
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: Matrix format
        uri: http://edamontology.org/format_3033
    - data:
        term: Sample annotation
        uri: http://edamontology.org/data_3113
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: Matrix format
        uri: http://edamontology.org/format_3033
    - data:
        term: Gene expression profile
        uri: http://edamontology.org/data_0928
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: Matrix format
        uri: http://edamontology.org/format_3033
    note: null
    operation:
    - term: Gene expression clustering
      uri: http://edamontology.org/operation_0313
    - term: Treemap visualisation
      uri: http://edamontology.org/operation_2942
    - term: Statistical calculation
      uri: http://edamontology.org/operation_2238
    - term: Principal component plotting
      uri: http://edamontology.org/operation_2939
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    output:
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: http://biit.cs.ut.ee/clustvis
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-07-02T09:12:33.297394Z'
  license: GPL-3.0
  link:
  - note: A code repository in github.
    type:
    - Repository
    url: https://github.com/taunometsalu/ClustVis
  maturity: null
  name: ClustVis
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: rrid
    value: RRID:SCR_017133
    version: null
  owner: user.1781877465
  publication:
  - doi: 10.1093/nar/gkv468
    metadata:
      abstract: 'The Principal Component Analysis (PCA) is a widely used method of
        reducing the dimensionality of highdimensional data, often followed by visualizing
        two of the components on the scatterplot. Although widely used, the method
        is lacking an easy-to-use web interface that scientists with little programming
        skills could use to make plots of their own data. The same applies to creating
        heatmaps: it is possible to add conditional formatting for Excel cells to
        show colored heatmaps, but for more advanced features such as clustering and
        experimental annotations, more sophisticated analysis tools have to be used.
        We present a web tool called ClustVis that aims to have an intuitive user
        interface. Users can upload data from a simple delimited text file that can
        be created in a spreadsheet program. It is possible to modify data processing
        methods and the final appearance of the PCA and heatmap plots by using drop-down
        menus, text boxes, sliders etc. Appropriate defaults are given to reduce the
        time needed by the user to specify input parameters. As an output, users can
        download PCA plot and heatmap in one of the preferred file formats. This web
        server is freely available at http://biit.cs.ut.ee/clustvis/.'
      authors:
      - name: Metsalu T.
      - name: Vilo J.
      citationCount: 2504
      date: '2015-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'ClustVis: A web tool for visualizing clustering of multivariate data
        using Principal Component Analysis and heatmap'
    note: null
    pmcid: PMC4489295
    pmid: '25969447'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  validated: 1
  version:
  - '1'
- accessibility: Open access
  additionDate: '2022-05-17T15:02:47.356289Z'
  biotoolsCURIE: biotools:sequencematrix
  biotoolsID: sequencematrix
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: meier@nus.edu.sg
    fundrefid: null
    gridid: null
    name: Rudolf Meier
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: David J. Lohman
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Gaurav Vaidya
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: Concatenation software for the fast assembly of multi-gene datasets
    with character set and codon information.
  documentation: []
  download: []
  editPermission:
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    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    output: []
  homepage: http://www.ggvaidya.com/taxondna/
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-07-02T09:12:32.063802Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/gaurav/taxondna
  - note: null
    type:
    - Other
    url: http://taxondna.sourceforge.net
  maturity: null
  name: SequenceMatrix
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: gaurav
  publication:
  - doi: 10.1111/J.1096-0031.2010.00329.X
    metadata:
      abstract: We present SequenceMatrix, software that is designed to facilitate
        the assembly and analysis of multi-gene datasets. Genes are concatenated by
        dragging and dropping FASTA, NEXUS, or TNT files with aligned sequences into
        the program window. A multi-gene dataset is concatenated and displayed in
        a spreadsheet; each sequence is represented by a cell that provides information
        on sequence length, number of indels, the number of ambiguous bases ("Ns"),
        and the availability of codon information. Alternatively, GenBank numbers
        for the sequences can be displayed and exported. Matrices with hundreds of
        genes and taxa can be concatenated within minutes and exported in TNT, NEXUS,
        or PHYLIP formats, preserving both character set and codon information for
        TNT and NEXUS files. SequenceMatrix also creates taxon sets listing taxa with
        a minimum number of characters or gene fragments, which helps assess preliminary
        datasets. Entire taxa, whole gene fragments, or individual sequences for a
        particular gene and species can be excluded from export. Data matrices can
        be re-split into their component genes and the gene fragments can be exported
        as individual gene files. SequenceMatrix also includes two tools that help
        to identify sequences that may have been compromised through laboratory contamination
        or data management error. One tool lists identical or near-identical sequences
        within genes, while the other compares the pairwise distance pattern of one
        gene against the pattern for all remaining genes combined. SequenceMatrix
        is Java-based and compatible with the Microsoft Windows, Apple MacOS X and
        Linux operating systems. The software is freely available from © The Willi
        Hennig Society 2010. © The Willi Hennig Society 2010.
      authors:
      - name: Vaidya G.
      - name: Lohman D.J.
      - name: Meier R.
      citationCount: 1348
      date: '2011-04-01T00:00:00Z'
      journal: Cladistics
      title: 'SequenceMatrix: Concatenation software for the fast assembly of multi-gene
        datasets with character set and codon information'
    note: null
    pmcid: null
    pmid: '34875773'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Genetics
    uri: http://edamontology.org/topic_3053
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2026-05-07T14:37:06.887814Z'
  biotoolsCURIE: biotools:bigr_xnattools
  biotoolsID: bigr_xnattools
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: m.starmans@erasmusmc.nl
    fundrefid: null
    gridid: null
    name: Martijn PA Starmans
    note: null
    orcidid: https://orcid.org/0000-0001-5086-7153
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://bigr.nl/member/martijn/
  - email: null
    fundrefid: null
    gridid: null
    name: Erasmus MC
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: 'xnattools is a python package with a set of modules for performing
    various operations on data stored in XNAT servers. The main purpose is to provide
    one standardized platform for running operations on XNAT servers. The package
    currently contains four tools that use this platform: dicom to nifty conversion,
    thumbnail generation from dicom, DICOM header data collection, in bulk downloading
    of a project.'
  documentation: []
  download:
  - note: null
    type: Source code
    url: https://gitlab.com/radiology/radiomics/xnattools
    version: v1.0.0
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data editing
      uri: http://edamontology.org/operation_3096
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Aggregation
      uri: http://edamontology.org/operation_3436
    output: []
  homepage: https://gitlab.com/radiology/radiomics/xnattools
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-07-02T07:58:30.527681Z'
  license: Apache-2.0
  link: []
  maturity: Emerging
  name: BIGR xnattools
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: erik_h.m.
  publication: []
  relation:
  - biotoolsID: xnatpy
    type: uses
  - biotoolsID: xnat
    type: uses
  toolType:
  - Library
  topic: []
  validated: 0
  version:
  - v1.0.0
- accessibility: Open access
  additionDate: '2026-06-23T15:47:38.017635Z'
  biotoolsCURIE: biotools:deeptaxa
  biotoolsID: deeptaxa
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: amoustafa@aucegypt.edu
    fundrefid: null
    gridid: null
    name: Ahmed Moustafa
    note: Professor at the American University in Cairo
    orcidid: https://orcid.org/0000-0002-0111-3555
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    url: https://ahmedmoustafa.github.io/
  - email: rana_salah@aucegypt.edu
    fundrefid: null
    gridid: null
    name: Rana Salah
    note: null
    orcidid: https://orcid.org/0000-0003-2344-0714
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: khlood.ramadan@aucegypt.edu
    fundrefid: null
    gridid: null
    name: Khlood R. AbdElaal
    note: null
    orcidid: https://orcid.org/0009-0009-0054-9283
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: lobnaghonaim@aucegypt.edu
    fundrefid: null
    gridid: null
    name: Lobna Ghonaim
    note: null
    orcidid: https://orcid.org/0009-0003-6158-0029
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: DeepTaxa is a hybrid CNN-BERT deep learning framework for multi-rank
    taxonomic classification of 16S rRNA gene sequences. It predicts all seven Linnaean
    ranks from domain to species in a single forward pass and provides pre-trained
    checkpoints for full-length 16S and V3-V4 amplicons.
  documentation:
  - note: 'Tutorials: prediction, training, analysis, architecture'
    type:
    - User manual
    url: https://systems-genomics-lab.github.io/deeptaxa/
  download:
  - note: 'PyPI: pip install deeptaxa-rrna'
    type: Software package
    url: https://pypi.org/project/deeptaxa-rrna/
    version: null
  - note: 'Bioconda: conda install -c bioconda deeptaxa-rrna'
    type: Software package
    url: https://anaconda.org/bioconda/deeptaxa-rrna
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output: []
  homepage: https://github.com/systems-genomics-lab/deeptaxa
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-07-01T19:35:41.530572Z'
  license: MIT
  link:
  - note: Source code
    type:
    - Repository
    url: https://github.com/systems-genomics-lab/deeptaxa
  - note: Bug reports and feature requests
    type:
    - Issue tracker
    url: https://github.com/systems-genomics-lab/deeptaxa/issues
  - note: Pre-trained model checkpoints
    type:
    - Other
    url: https://huggingface.co/systems-genomics-lab/deeptaxa
  maturity: Emerging
  name: DeepTaxa
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: ahmed7
  publication:
  - doi: 10.1093/bioadv/vbag166
    metadata: null
    note: null
    pmcid: PMC13316423
    pmid: '42381921'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  validated: 0
  version:
  - 1.0.1
- accessibility: null
  additionDate: '2026-06-29T22:57:54.304323Z'
  biotoolsCURIE: biotools:babel
  biotoolsID: babel
  collectionID: []
  confidence_flag: null
  cost: Free of charge
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