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  description: MicroMiner assists in identifying single-residue substitutions in protein
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  - note: null
    type:
    - General
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  function:
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      format:
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    - data:
        term: UniProt accession
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      format: []
    - data:
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    - term: Local structure alignment
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    - term: Structure database search
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    - data:
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    - data:
        term: Protein structure
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      - term: PDB
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    - data:
        term: Database search results
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      format:
      - term: Textual format
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  language: []
  lastUpdate: '2026-06-16T12:37:05.019651Z'
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  link:
  - note: A web service to run MicroMiner calculations for protein structures stored
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  - term: Drug discovery
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  - term: Data mining
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  - term: Bioinformatics
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  description: The ProteinsPlus web server aims to support life scientists in working
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    The poses can then be visualized in 2D (PoseView, PoseEdit). Furthermore, advanced
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    metal coordination (METALizer), the analysis of solvent channels in protein crystals
    (LifeSoaks), or the categorization of protein-protein-interfaces (HyPPI) are supported.
  documentation:
  - note: null
    type:
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  function:
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    input:
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    note: prediction of protonation states and tautomers and placement of hydrogen
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    operation:
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  - cmd: null
    input:
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  - cmd: null
    input:
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    - data:
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    note: calculating bottleneck radii for crystal solvent channels
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  - cmd: null
    input:
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      format:
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      format:
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      - term: SDF
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    - data:
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        uri: http://edamontology.org/data_1463
      format:
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        uri: http://edamontology.org/format_3814
    note: atom-level assessment of the electron density fit for structures solved
      by X-ray crystallography
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    - term: Data filtering
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    output:
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      format:
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    input:
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    note: protein-protein interface classification (permanent, transient, crystal
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    operation:
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  - cmd: null
    input:
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      format:
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    note: protein-ligand docking for small molecules
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    - term: Protein-ligand docking
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    - term: Protein-metal contact calculation
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    - term: Protein modelling
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    output:
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      - term: SDF
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    - data:
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    - data:
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      format:
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        uri: http://edamontology.org/format_3814
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    - data:
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      format: []
  - cmd: null
    input:
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        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
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        uri: http://edamontology.org/format_1476
    - data:
        term: Protein-ligand complex
        uri: http://edamontology.org/data_1461
      format:
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        uri: http://edamontology.org/format_1476
      - term: SDF
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    - data:
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      format:
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    note: small molecule binding site detection
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    - term: Protein modelling
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    output:
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      format:
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        uri: http://edamontology.org/format_1476
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      format:
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        uri: http://edamontology.org/format_2330
    - data:
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      format: []
  - cmd: null
    input:
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      format:
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      format:
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    - data:
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      format:
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    note: small molecule binding site detection and druggability assessment
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    - term: Protein modelling
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    - term: Protein structure analysis
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    output:
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      format:
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  - cmd: null
    input:
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    note: 2D interaction diagram drawing and editing
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    - term: Salt bridge calculation
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    - term: Hydrogen bond calculation
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    output:
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        uri: http://edamontology.org/data_1566
      format:
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      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
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        uri: http://edamontology.org/data_2992
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      - term: JSON
        uri: http://edamontology.org/format_3464
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      - term: JSON
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    input:
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    - data:
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    note: metal complex geometry prediction
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    - term: Protein-metal contact calculation
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    - term: Protein structure analysis
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    output:
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      format:
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  description: JAMDA enables the preparation of individual protein structures and
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  description: Three-dimensional protein structures play a vital role in drug design.
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  description: LifeSoaks was designed to find solvent channels in macromolecular structures
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  description: METALizer predicts the coordination geometry of metal ions in metalloproteins.
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  description: The electron density score for individual atoms (EDIA) quantifies the
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  description: SIENA is a software pipeline enabling the fully automated construction
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  description: DoGSiteScorer is a grid-based automated pocket detection and analysis
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    note: Web calculator for OD260, mass, and molar conversion across nucleic acids
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  - note: null
    type:
    - Repository
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  - note: null
    type:
    - Service
    url: https://www.pepkio.com/tools/mendelian-cross-solver
  - note: null
    type:
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  operatingSystem: []
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  publication: []
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  toolType:
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  - Web application
  - Command-line tool
  topic:
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    uri: http://edamontology.org/topic_3053
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2026-06-15T07:22:14.272830Z'
  biotoolsCURIE: biotools:pepkio-hwe-equilibrium-studio
  biotoolsID: pepkio-hwe-equilibrium-studio
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
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    name: Pepkio
    note: Pepkio develops software tools and bioinformatics solutions for life science
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    orcidid: null
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    typeEntity: Project
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  description: Evaluates Hardy-Weinberg equilibrium for diploid loci with two to six
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  documentation:
  - note: null
    type:
    - General
    url: https://www.pepkio.com/tools/hwe-equilibrium-studio
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    type:
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    note: Web calculator for multiallelic HWE testing and Wright-Fisher simulation;
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      uri: http://edamontology.org/operation_0554
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  language:
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  lastUpdate: '2026-06-15T07:22:14.277319Z'
  license: MIT
  link:
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    type:
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  - note: null
    type:
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  maturity: null
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  toolType:
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  - Library
  topic:
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  - term: Genetics
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  - term: Genotype and phenotype
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  additionDate: '2026-06-15T06:59:04.569639Z'
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    name: Pepkio
    note: Pepkio develops software tools and bioinformatics solutions for life science
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    orcidid: null
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    typeEntity: Project
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  description: Performs batch four-parameter and five-parameter logistic regression
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    Hill slope, and related potency metrics with per-compound QC grades. A browser
    calculator supports CSV upload, curve review, and figure export; a Python library
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  documentation:
  - note: null
    type:
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    url: https://www.pepkio.com/tools/dose-curve-fitter
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    type:
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  function:
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    note: Web calculator for HTS dose–response fitting; Python library and CLI for
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    - term: Regression analysis
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    output: []
  homepage: https://www.pepkio.com/tools/dose-curve-fitter
  homepage_status: 0
  language:
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  lastUpdate: '2026-06-15T06:59:56.154599Z'
  license: MIT
  link:
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    type:
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    url: https://github.com/pepkio/pepkio-dose-curve-fitter
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    type:
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  operatingSystem: []
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  owner: pepkio
  publication: []
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  toolType:
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  - Command-line tool
  - Library
  topic:
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  - term: Molecular biology
    uri: http://edamontology.org/topic_3047
  - term: Laboratory techniques
    uri: http://edamontology.org/topic_3361
  validated: 0
  version:
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- accessibility: null
  additionDate: '2026-06-14T11:27:33.179639Z'
  biotoolsCURIE: biotools:seqbench-online
  biotoolsID: seqbench-online
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: SeqBench is a free collection of browser-based tools for working with
    DNA, RNA and protein sequences, including reverse complement, translation, ORF
    finding, GC content, primer melting temperature, restriction site analysis, codon
    optimization, pairwise alignment and plasmid visualization. All computation runs
    client-side in the browser, so input sequences are never uploaded to a server.
  documentation: []
  download: []
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    input: []
    note: null
    operation:
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    - term: DNA translation
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    - term: PCR primer design
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    - term: Sequence composition calculation
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    - term: Sequence alignment
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    output: []
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  homepage_status: 0
  language: []
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  license: Freeware
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  maturity: Emerging
  name: SeqBench
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  owner: SeqBench
  publication: []
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0080
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-06-14T08:34:19.506926Z'
  biotoolsCURIE: biotools:phylo-movies
  biotoolsID: phylo-movies
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Enes Berk Sakalli
    note: Corresponding software contact.
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: https://github.com/enesBerkSakalli
  - email: null
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    gridid: null
    name: Simon E. Haendeler
    note: null
    orcidid: null
    rorid: null
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    rorid: null
    typeEntity: Person
    typeRole:
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  - email: null
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  description: Phylo-Movies is an open-source React and Flask web application, also
    available as a desktop app, for inspecting ordered phylogenetic tree series. It
    computes and visualizes subtree-prune-and-regraft transition frames between consecutive
    trees, helping users see which taxa or subtrees move across sliding-window analyses,
    bootstrap replicates, and curated tree-series comparisons. The viewer includes
    timeline playback, tree comparison, MSA context, coloring, analytics, image export,
    and recording tools.
  documentation:
  - note: Researcher-facing manual.
    type:
    - User manual
    url: https://enesberksakalli.github.io/phylo-movies/manual/
  - note: Project overview, installation, usage, citation, and links.
    type:
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    url: https://github.com/enesBerkSakalli/phylo-movies/blob/main/README.md
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    type:
    - Installation instructions
    url: https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/getting-started.md
  - note: Backend API documentation.
    type:
    - API documentation
    url: https://github.com/enesBerkSakalli/phylo-movies/blob/main/docs/api.md
  download:
  - note: Source checkout for full web application and backend workflows.
    type: Source code
    url: https://github.com/enesBerkSakalli/phylo-movies
    version: 0.98.1
  - note: Desktop convenience builds for macOS, Windows, and Linux.
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    url: https://github.com/enesBerkSakalli/phylo-movies/releases/tag/v0.98.1
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  function:
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    input:
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    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
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      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Visualizes ordered phylogenetic tree series as animated transition movies
      with comparison, MSA context, movement analytics, image export, and recording
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    operation:
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    output:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
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        uri: http://edamontology.org/format_1910
      - term: JSON
        uri: http://edamontology.org/format_3464
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  homepage_status: 0
  language:
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  - JavaScript
  - TypeScript
  lastUpdate: '2026-06-14T08:36:42.066838Z'
  license: MIT
  link:
  - note: Source code repository.
    type:
    - Repository
    url: https://github.com/enesBerkSakalli/phylo-movies
  - note: Static browser demo with precomputed example movies.
    type:
    - Service
    url: https://enesberksakalli.github.io/phylo-movies/demo/
  - note: null
    type:
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    url: https://github.com/enesBerkSakalli/phylo-movies/issues
  maturity: Mature
  name: Phylo-Movies
  operatingSystem:
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  - Mac
  - Linux
  otherID: []
  owner: enes
  publication:
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    metadata: null
    note: bioRxiv preprint describing the Phylo-Movies method and examples.
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  - doi: 10.5281/zenodo.20488923
    metadata: null
    note: Archived software release on Zenodo.
    pmcid: null
    pmid: null
    type:
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    version: 0.98.1
  relation: []
  toolType:
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  - Web application
  topic:
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  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2026-06-12T15:37:36.437343Z'
  biotoolsCURIE: biotools:lacuna
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  description: 'When a stroke, tumor, or other focal brain injury damages tissue,
    understanding its consequences requires placing the lesion within the broader
    organization of the brain. Lacuna is an open-source toolbox that uses normative
    reference data from healthy individuals, including connectivity datasets and anatomical
    atlases, to characterize lesions beyond their anatomical location.


    Users provide lesion masks in MNI space, and Lacuna automatically retrieves reference
    data, performs required processing steps, and generates BIDS-organized outputs.
    Designed for multicenter research, it standardizes workflows, scales from single
    cases to large cohorts, supports HPC deployment through containers, and records
    provenance for reproducible lesion analyses.'
  documentation:
  - note: null
    type:
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  license: null
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  operatingSystem:
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  publication: []
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  topic:
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  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-06-12T12:09:48.272845Z'
  biotoolsCURIE: biotools:nallo
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  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
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    fundrefid: null
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  description: 'Nallo is a bioinformatics analysis pipeline for long-reads from both
    PacBio and (targeted) ONT-data, focused on rare-disease. The pipeline detects
    a wide range of genetic variants, performs genome assembly,

    and reports CpG methylation. It also enables annotation and ranking of variants
    based on their predicted functional

    consequences.'
  documentation:
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    type:
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  function:
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    input:
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        term: Sequence alignment
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        uri: http://edamontology.org/format_3752
      - term: BAM
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      - term: FASTQ-like format
        uri: http://edamontology.org/format_2545
    note: null
    operation:
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    - term: Variant effect prediction
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    output:
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      - term: BAI
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  homepage_status: 0
  language:
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  lastUpdate: '2026-06-12T14:03:07.797466Z'
  license: MIT
  link:
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    type:
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  maturity: null
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  publication:
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    metadata: null
    note: null
    pmcid: PMC12988770
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    type: []
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  topic:
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  - term: Whole genome sequencing
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  - term: Transcription factors and regulatory sites
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  - term: Epigenetics
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  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2026-06-12T12:35:12.904681Z'
  biotoolsCURIE: biotools:derr
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    note: null
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  description: DeRR (Detection Dual T-cell receptor in single cell sequencing) is
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    dual-TCR in scRNA-Seq/scTCR-Seq.
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  download:
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  function:
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    note: Demultiplex sequence data
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  - cmd: python DeRR.py [OPTIONS]
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    note: AIRR compatible V-J gene calling
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    output:
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    - data:
        term: Sequence property
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  lastUpdate: '2026-06-12T13:26:08.934404Z'
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    type:
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  publication:
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    type:
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    version: null
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  topic:
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  validated: 0
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- accessibility: null
  additionDate: '2017-08-03T18:52:54Z'
  biotoolsCURIE: biotools:obitools
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  description: Set of python programs developed to simplify the manipulation of sequence
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next: ?page=2
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