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  description: Interactive browser for the complete Human Phenotype Ontology (~19,800
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  download:
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  biotoolsCURIE: biotools:smiles-mapper
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  description: SMILES-Mapper is a small web app that allows students to easily visualize
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  language:
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  license: MIT
  link:
  - note: URL for web-app, where SMILES-Mapper can be used for free.
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  biotoolsCURIE: biotools:platforma
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  description: 'Integrated software platform for biologics discovery and NGS analysis,
    supporting antibody discovery, peptide discovery, TCR/BCR repertoire profiling,
    and multi-omics data integration. Built on MiXCR, a widely adopted tool for adaptive
    immune repertoire sequencing, and other open-source bioinformatics algorithms.


    In vitro antibody discovery: Computational analysis of display-based selection
    (e.g., phage/yeast display) NGS datasets to identify enriched antibody sequences,
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    features and developability metrics, supported by ML-based ranking workflows.


    In vivo antibody discovery: Integration of immune repertoire sequencing with functional
    assay outputs and developability annotations to characterize adaptive immune responses,
    identify antigen-associated clonotypes, and prioritize lead antibody candidates
    through multi-parameter computational scoring and repertoire-level analysis.'
  documentation:
  - note: null
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  - term: Proteins
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  - term: Sequence assembly
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  - term: Bioinformatics
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  - term: Genomics
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  - term: Multiomics
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  biotoolsCURIE: biotools:squarna
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  collectionID:
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  confidence_flag: tool
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Eugene F Baulin
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  description: SQUARNA is a tool for RNA secondary structure prediction. It can take
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  validated: 0
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- accessibility: null
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  description: PLIP is a tool for fast identification of non-covalent interactions
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  description: pMLST is a tool developed by the Center for Genomic Epidemiology for
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  - term: Public health and epidemiology
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  - term: Sequence assembly
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  - term: Zoology
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  - R
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    type:
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  name: miRcounts
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  additionDate: '2015-01-22T11:13:24Z'
  biotoolsCURIE: biotools:clustvis
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  description: Web tool which allows users to upload their own data and easily create
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  documentation:
  - note: null
    type:
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    version: null
  editPermission:
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  elixirPlatform:
  - Tools
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  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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  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: null
  additionDate: '2026-03-13T13:09:40.841224Z'
  biotoolsCURIE: biotools:snapgene
  biotoolsID: snapgene
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Tool to intuitively design, simulate, and visualise plasmids, primers,
    and DNA constructs.
  documentation: []
  download: []
  editPermission:
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  homepage: https://www.snapgene.com/
  homepage_status: 0
  language: []
  lastUpdate: '2026-07-02T09:12:22.360898Z'
  license: null
  link: []
  maturity: null
  name: SnapGene
  operatingSystem: []
  otherID: []
  owner: samaa
  publication: []
  relation: []
  toolType: []
  topic: []
  validated: 0
  version:
  - '8.2'
- accessibility: null
  additionDate: '2016-10-03T14:08:36Z'
  biotoolsCURIE: biotools:mdweb
  biotoolsID: mdweb
  collectionID:
  - BioExcel
  - IRB-BSC
  - ELIXIR-ES
  confidence_flag: null
  cost: Free of charge (with restrictions)
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Institute of Research in Biomedicine - Barcelona
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole: []
    url: null
  - email: mdweb@mmb.irbbarcelona.org
    fundrefid: null
    gridid: null
    name: Institute for Research in Biomedicine Barcelona
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: Web-based platform to help access to molecular dynamics (MD). The platform
    provides tools to prepare systems from PDB structures mimicking the procedures
    followed by human experts. It provides inputs and can send simulations for three
    of the most popular MD packages (Amber, NAMD and Gromacs). Tools for analysis
    of trajectories are also incorporated.
  documentation:
  - note: null
    type:
    - User manual
    - Training material
    url: http://mmb.irbbarcelona.org/MDWeb2/help.php?id=base
  download: []
  editPermission:
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    - gelpi@ub.edu
    - rutupatel
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  elixir_badge: 0
  function:
  - cmd: null
    input:
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        term: PDB ID
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      format:
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        uri: http://edamontology.org/format_1964
    - data:
        term: Structure
        uri: http://edamontology.org/data_0883
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Platform for setup and analysis of molecular dynamics simulations
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Molecular dynamics
      uri: http://edamontology.org/operation_2476
    output: []
  homepage: http://mmb.irbbarcelona.org/MDWeb2
  homepage_status: 0
  language:
  - PHP
  lastUpdate: '2026-07-02T09:12:20.161140Z'
  license: null
  link: []
  maturity: Mature
  name: MDWeb
  operatingSystem:
  - Linux
  otherID: []
  owner: jdianes
  publication:
  - doi: 10.1093/bioinformatics/bts139
    metadata:
      abstract: MDWeb and MDMoby constitute a web-based platform to help access to
        molecular dynamics (MD) in the standard and high-throughput regime. The platform
        provides tools to prepare systems from PDB structures mimicking the procedures
        followed by human experts. It provides inputs and can send simulations for
        three of the most popular MD packages (Amber, NAMD and Gromacs). Tools for
        analysis of trajectories, either provided by the user or retrieved from our
        MoDEL database (http://mmb.pcb.ub.es/MoDEL) are also incorporated. The platform
        has two ways of access, a set of web-services based on the BioMoby framework
        (MDMoby), programmatically accessible and a web portal (MDWeb). © The Author
        2012. Published by Oxford University Press. All rights reserved.
      authors:
      - name: Hospital A.
      - name: Andrio P.
      - name: Fenollosa C.
      - name: Cicin-Sain D.
      - name: Orozco M.
      - name: Gelpi J.L.
      citationCount: 147
      date: '2012-05-01T00:00:00Z'
      journal: Bioinformatics
      title: 'MDWeb and MDMoby: An integrated web-based platform for molecular dynamics
        simulations'
    note: null
    pmcid: null
    pmid: '22437851'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Workbench
  topic:
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Biophysics
    uri: http://edamontology.org/topic_3306
  - term: Molecular dynamics
    uri: http://edamontology.org/topic_0176
  - term: Molecular modelling
    uri: http://edamontology.org/topic_2275
  validated: 1
  version:
  - '2.0'
- 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:
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  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:
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    - 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:
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    url: null
  - email: khlood.ramadan@aucegypt.edu
    fundrefid: null
    gridid: null
    name: Khlood R. AbdElaal
    note: null
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    typeRole:
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  - email: lobnaghonaim@aucegypt.edu
    fundrefid: null
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    name: Lobna Ghonaim
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    orcidid: https://orcid.org/0009-0003-6158-0029
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    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:
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  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: '2026-07-01T09:38:06.880438Z'
  biotoolsCURIE: biotools:mirnaprotpred
  biotoolsID: mirnaprotpred
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: somenath@pusan.ac.kr
    fundrefid: null
    gridid: null
    name: Somenath Dutta
    note: null
    orcidid: https://orcid.org/0000-0002-9580-6386
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://somenath.biounfold.in/
  description: 'A powerful, high-performance bioinformatics framework for discovering,
    evaluating, and verifying microRNA (miRNA) interactions across DNA, RNA, and protein
    target sequences.


    The mirnaprotpred package provides two core modules:


    SeqFinder: A discovery engine to find all potential miRNA interactions across
    a genome or target sequence.

    Validator: A targeted verification engine to test specific, user-provided miRNAs
    against a target sequence.

    Both modules are powered by a shared, rigorous biological engine that evaluates
    exact seed matching, wobble pairing, AU-rich context, and RNAduplex thermodynamic
    stability.'
  documentation:
  - note: null
    type:
    - User manual
    url: https://mirnaprotpred.biounfold.in/
  download: []
  editPermission:
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    type: private
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  function: []
  homepage: https://mirnaprotpred.biounfold.in/
  homepage_status: 0
  language: []
  lastUpdate: '2026-07-01T09:38:19.203211Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/somenath-combio/mirnaprotpred/
  maturity: null
  name: miRNAProtPred
  operatingSystem:
  - Windows
  - Mac
  - Linux
  otherID: []
  owner: somenath
  publication:
  - doi: 10.3389/fgene.2026.1817432
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-07-01T06:23:45.238507Z'
  biotoolsCURIE: biotools:3d-cancer-model-development-services
  biotoolsID: 3d-cancer-model-development-services
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: To this date, numerous developments, like organoids, in 3D culturing
    technology, have made creating novel, more physiological human cancer models possible.
    At Alfa Cytology, we focus on developing 3D cancer models and aim to provide researchers
    and scientists working in oncology with cutting-edge tools. Our services help
    clients streamline their drug discovery process and further their knowledge of
    cancer biology.
  documentation: []
  download: []
  editPermission:
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    type: private
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  elixir_badge: 0
  function: []
  homepage: https://www.alfacytology.com/3d-cancer-models/3d-cancer-model-development-services.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-07-01T06:24:01.755423Z'
  license: null
  link: []
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next: ?page=2
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