count: 4132
list:
- accessibility: Open access
  additionDate: '2026-05-20T08:59:02.212508Z'
  biotoolsCURIE: biotools:snp-sites
  biotoolsID: snp-sites
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Finds SNP sites from a multi-FASTA alignment file.
  documentation:
  - note: null
    type:
    - General
    url: https://sanger-pathogens.github.io/snp-sites/
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: 'snp-sites my_alignment.aln

      snp-sites my_gzipped_alignment.aln.gz'
    input:
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        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: Relaxed PHYLIP Sequential
        uri: http://edamontology.org/format_3820
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: null
    operation:
    - term: SNP detection
      uri: http://edamontology.org/operation_0484
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: Relaxed PHYLIP Sequential
        uri: http://edamontology.org/format_3820
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://sanger-pathogens.github.io/snp-sites/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-05-20T08:59:02.214591Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/sanger-pathogens/snp-sites
  maturity: null
  name: SNP-sites
  operatingSystem:
  - Linux
  otherID: []
  owner: aniehues
  publication:
  - doi: 10.1099/mgen.0.000056
    metadata: null
    note: null
    pmcid: PMC5320690
    pmid: '28348851'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  validated: 0
  version:
  - 2.5.1
- accessibility: Open access
  additionDate: '2026-05-19T21:38:22.336113Z'
  biotoolsCURIE: biotools:parsesnp21-26
  biotoolsID: parsesnp21-26
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: A small <720Kb C++ windows utility. That allows you to load  Ancestry,
    23andMe, FTDNA, or Genes for Good RAW DNA files search them, merge them. covert
    them to Ancestry format. But also create files from peer reviewed publications
    to compare with you loaded data to give your genetic disposition for the condition
    you have entered the data for an statistical risk if OR values are included. Included
    with the program are example files for Type 2 Diabetes risk factors. (As I have
    type 2 Diabetes so I could test the results).
  documentation:
  - note: pdf user manual
    type:
    - User manual
    url: https://raw.githubusercontent.com/BritRobin/ParseSNP/master/ParseSNP_Manual.pdf
  download:
  - note: Windows x64 or x86 installer
    type: Software package
    url: https://britrobin.github.io/ParseSNP/
    version: 1.1.1
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://britrobin.github.io/ParseSNP/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-05-20T00:58:03.254713Z'
  license: GPL-3.0
  link:
  - note: Git page for easy installer and pdf manual  download
    type:
    - Other
    url: https://britrobin.github.io/ParseSNP/
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/BritRobin/ParseSNP
  maturity: Emerging
  name: ParseSNP
  operatingSystem:
  - Windows
  otherID: []
  owner: RobinTaylor
  publication: []
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Personalised medicine
    uri: http://edamontology.org/topic_3577
  validated: 0
  version:
  - 1.1.1
- accessibility: Open access
  additionDate: '2026-05-20T00:15:17.437872Z'
  biotoolsCURIE: biotools:compucell3d
  biotoolsID: compucell3d
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: CompuCell3D is a multiscale multicellular virtual tissue modeling and
    simulation environment. CompuCell3D is written in C++ and provides Python bindings
    for model and simulation development in Python.
  documentation:
  - note: null
    type:
    - API documentation
    url: https://compucell3d.org/
  - note: null
    type:
    - Training material
    url: https://compucell3d.org/Tutorials
  - note: null
    type:
    - Citation instructions
    url: https://compucell3d.org/Publications
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output: []
  homepage: https://compucell3d.org/SrcBin
  homepage_status: 0
  language:
  - Python
  - C++
  lastUpdate: '2026-05-20T00:31:43.306086Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://compucell3d.org/SrcBin
  - note: null
    type:
    - Discussion forum
    url: https://www.reddit.com/r/CompuCell3D/
  maturity: Mature
  name: CompuCell3D
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: VKasalica
  publication:
  - doi: 10.1016/b978-0-12-388403-9.00013-8
    metadata: null
    note: null
    pmcid: PMC3612985
    pmid: '22482955'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  validated: 0
  version:
  - 4.8.0
- accessibility: Open access
  additionDate: '2026-05-20T00:01:38.156396Z'
  biotoolsCURIE: biotools:nuclearphaser
  biotoolsID: nuclearphaser
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jana Sperschneider
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://github.com/JanaSperschneider
  description: NuclearPhaser is a method for phasing of dikaryotic genomes into the
    two haplotypes using Hi-C contact graphs. This is an overview of the phasing pipeline
    for dikaryons.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/JanaSperschneider/NuclearPhaser/blob/main/README.md
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output: []
  homepage: https://github.com/JanaSperschneider/NuclearPhaser
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-20T00:10:43.605604Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/JanaSperschneider/NuclearPhaser
  maturity: Emerging
  name: NuclearPhaser
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: VKasalica
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - '1.1'
- accessibility: null
  additionDate: '2026-05-06T23:40:03.794540Z'
  biotoolsCURIE: biotools:generode
  biotoolsID: generode
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Workflow for whole genome sequencing analysis, including patterns of
    genome erosion. Written in Snakemake workflow language.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/NBISweden/GenErode
  - note: null
    type:
    - User manual
    url: https://github.com/NBISweden/GenErode/wiki
  download: []
  editPermission:
    authors: []
    type: public
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence masking
      uri: http://edamontology.org/operation_0368
    - term: Genome indexing
      uri: http://edamontology.org/operation_3211
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: BED
        uri: http://edamontology.org/format_3003
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Read mapping
      uri: http://edamontology.org/operation_3198
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    - term: Nucleic acid sequence analysis
      uri: http://edamontology.org/operation_2478
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
    note: null
    operation:
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://github.com/NBISweden/GenErode
  homepage_status: 0
  language:
  - Other
  lastUpdate: '2026-05-06T23:40:03.797298Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: GenErode
  operatingSystem: []
  otherID: []
  owner: johangustafsson
  publication:
  - doi: 10.1186/s12859-022-04757-0
    metadata: null
    note: null
    pmcid: PMC9195343
    pmid: '35698034'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-04-20T07:37:48.758499Z'
  biotoolsCURIE: biotools:biokanga
  biotoolsID: biokanga
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: BioKanga is an integrated toolkit of high performance bioinformatics
    subprocesses targeting the challenges of next generation sequencing analytics.
    Kanga is an acronym standing for 'K-mer Adaptive Next Generation Aligner'.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Statistical inference
      uri: http://edamontology.org/operation_3658
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Data deposition
      uri: http://edamontology.org/operation_3431
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    output: []
  homepage: https://github.com/csiro-crop-informatics/biokanga
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-04-20T07:37:48.760540Z'
  license: GPL-3.0
  link: []
  maturity: Emerging
  name: biokanga
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: veitveit11
  publication: []
  relation: []
  toolType:
  - Suite
  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version:
  - 4.4.2
- accessibility: null
  additionDate: '2018-08-13T22:07:48Z'
  biotoolsCURIE: biotools:picopore
  biotoolsID: picopore
  collectionID:
  - Bioconda
  - Python Software Foundation
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Scott Gigante
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Reduce the size of Oxford Nanopore Technologies' datasets without losing
    information.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function: []
  homepage: https://github.com/scottgigante/picopore
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-04-15T09:48:35.227827Z'
  license: GPL-3.0
  link:
  - note: Bioconda package
    type:
    - Repository
    url: https://anaconda.org/bioconda/picopore
  - note: Python Software Foundation
    type:
    - Repository
    url: https://pypi.org/project/picopore/
  maturity: null
  name: Picopore
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: aotamendi.1
  publication:
  - doi: 10.12688/f1000research.11022.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 1
  version:
  - 1.2.0
- accessibility: Open access
  additionDate: '2019-05-27T16:59:15Z'
  biotoolsCURIE: biotools:SLiM_software
  biotoolsID: SLiM_software
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: messer@cornell.edu
    fundrefid: null
    gridid: null
    name: Philipp Messer
    note: null
    orcidid: https://orcid.org/0000-0001-8453-9377
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: https://messerlab.org
  - email: bhaller@benhaller.com
    fundrefid: null
    gridid: null
    name: Benjamin C. Haller
    note: null
    orcidid: https://orcid.org/0000-0003-1874-8327
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://benhaller.com
  description: Evolutionary simulation framework that combines a powerful engine for
    population genetic simulations with the capability of modeling arbitrarily complex
    evolutionary scenarios.  Includes a graphical modeling environment.
  documentation:
  - note: The manual for SLiM itself
    type:
    - User manual
    url: http://benhaller.com/slim/SLiM_Manual.pdf
  - note: The manual for Eidos, the scripting language used by SLiM
    type:
    - User manual
    url: http://benhaller.com/slim/Eidos_Manual.pdf
  - note: Quick reference sheets for SLiM and Eidos
    type:
    - Quick start guide
    url: http://benhaller.com/slim/SLiMEidosRefSheets.zip
  download:
  - note: A source archive for the command-line `slim` tool only.  Complete source
      code is on GitHub, but most platforms have an installer anyway; see the manual,
      chapter 2, for installation instructions.
    type: Source code
    url: http://benhaller.com/slim/SLiM.zip
    version: null
  - note: The GitHub page for the current release version, to obtain full source code.
    type: Downloads page
    url: https://github.com/MesserLab/SLiM/releases/latest
    version: null
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Run individual-based eco-evolutionary simulations with explicit genetics
    operation:
    - term: Sequence generation
      uri: http://edamontology.org/operation_0230
    - term: DNA substitution modelling
      uri: http://edamontology.org/operation_0550
    - term: Ecological modelling
      uri: http://edamontology.org/operation_3946
    output: []
  homepage: https://messerlab.org/slim/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-04-13T17:54:54.015039Z'
  license: GPL-3.0
  link:
  - note: SLiM home page in the Messer Lab website
    type:
    - Software catalogue
    url: https://messerlab.org/slim/
  - note: GitHub repository for SLiM
    type:
    - Repository
    url: https://github.com/MesserLab/SLiM
  - note: Discussion forum for SLiM questions
    type:
    - Discussion forum
    url: https://groups.google.com/g/slim-discuss
  - note: Announcements mailing list
    type:
    - Mailing list
    url: https://groups.google.com/g/slim-announce
  maturity: Mature
  name: SLiM
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: bchaller
  publication:
  - doi: 10.1093/molbev/msy228
    metadata: null
    note: 'B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond
      the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.'
    pmcid: PMC6389312
    pmid: '30517680'
    type:
    - Primary
    version: '3.0'
  - doi: 10.1093/molbev/msy237
    metadata: null
    note: B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners.
      Molecular Biology and Evolution 36(5), 1101–1109.
    pmcid: PMC6501880
    pmid: '30590560'
    type:
    - Method
    version: '3.0'
  - doi: 10.1111/1755-0998.12968
    metadata: null
    note: B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019).
      Tree-sequence recording in SLiM opens new horizons for forward-time simulation
      of whole genomes. Molecular Ecology Resources 19(2), 552–566.
    pmcid: PMC6393187
    pmid: '30565882'
    type:
    - Primary
    version: '3.0'
  - doi: 10.1101/2025.08.07.669155
    metadata: null
    note: 'BC Haller, PL Ralph, PW Messer. (2025). SLiM 5: Eco-evolutionary simulations
      across multiple chromosomes and full genomes. bioRxiv, 2025.08. 07.669155'
    pmcid: PMC12363870
    pmid: '40832315'
    type:
    - Primary
    version: '5.0'
  - doi: 10.1086/723601
    metadata: null
    note: 'B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary
      modeling. The American Naturalist 201(5), E127–E139.'
    pmcid: PMC10793872
    pmid: '37130229'
    type:
    - Primary
    version: '4.0'
  relation: []
  toolType:
  - Command-line tool
  - Desktop application
  topic:
  - term: Ecology
    uri: http://edamontology.org/topic_0610
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  validated: 0
  version:
  - '5.2'
- accessibility: null
  additionDate: '2017-08-20T17:18:10Z'
  biotoolsCURIE: biotools:provean
  biotoolsID: provean
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://provean.jcvi.org/contact.php
  description: A software tool which predicts whether an amino acid substitution or
    indel has an impact on the biological function of a protein.
  documentation:
  - note: null
    type:
    - General
    url: http://provean.jcvi.org/index.php
  download: []
  editPermission:
    authors:
    - animalandcropgenomics
    - ahmad_raza
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Sequence annotation
      uri: http://edamontology.org/operation_0361
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    output: []
  homepage: http://provean.jcvi.org/index.php
  homepage_status: 0
  language:
  - Shell
  lastUpdate: '2026-03-30T09:22:11.430833Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: PROVEAN
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: ahmad_raza
  publication:
  - doi: 10.1371/journal.pone.0046688
    metadata:
      abstract: As next-generation sequencing projects generate massive genome-wide
        sequence variation data, bioinformatics tools are being developed to provide
        computational predictions on the functional effects of sequence variations
        and narrow down the search of casual variants for disease phenotypes. Different
        classes of sequence variations at the nucleotide level are involved in human
        diseases, including substitutions, insertions, deletions, frameshifts, and
        non-sense mutations. Frameshifts and non-sense mutations are likely to cause
        a negative effect on protein function. Existing prediction tools primarily
        focus on studying the deleterious effects of single amino acid substitutions
        through examining amino acid conservation at the position of interest among
        related sequences, an approach that is not directly applicable to insertions
        or deletions. Here, we introduce a versatile alignment-based score as a new
        metric to predict the damaging effects of variations not limited to single
        amino acid substitutions but also in-frame insertions, deletions, and multiple
        amino acid substitutions. This alignment-based score measures the change in
        sequence similarity of a query sequence to a protein sequence homolog before
        and after the introduction of an amino acid variation to the query sequence.
        Our results showed that the scoring scheme performs well in separating disease-associated
        variants (n = 21,662) from common polymorphisms (n = 37,022) for UniProt human
        protein variations, and also in separating deleterious variants (n = 15,179)
        from neutral variants (n = 17,891) for UniProt non-human protein variations.
        In our approach, the area under the receiver operating characteristic curve
        (AUC) for the human and non-human protein variation datasets is ~0.85. We
        also observed that the alignment-based score correlates with the deleteriousness
        of a sequence variation. In summary, we have developed a new algorithm, PROVEAN
        (Protein Variation Effect Analyzer), which provides a generalized approach
        to predict the functional effects of protein sequence variations including
        single or multiple amino acid substitutions, and in-frame insertions and deletions.
        The PROVEAN tool is available online at http://provean.jcvi.org. © 2012 Choi
        et al.
      authors:
      - name: Choi Y.
      - name: Sims G.E.
      - name: Murphy S.
      - name: Miller J.R.
      - name: Chan A.P.
      citationCount: 2199
      date: '2012-10-08T00:00:00Z'
      journal: PLoS ONE
      title: Predicting the Functional Effect of Amino Acid Substitutions and Indels
    note: null
    pmcid: PMC3466303
    pmid: '23056405'
    type:
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    version: null
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  validated: 1
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  description: QuaC is a snakemake-based pipeline that runs several QC tools for WGS/WES
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  description: Rosalution assists researchers study genetic variation 🧬 in patients
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  description: RhizoVision Explorer is free and open-source software developed for
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    metadata:
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        cycle. Root characteristics like length, diameter and volume are critical
        to measure to understand plant and soil functions. RhizoVision Explorer is
        an open-source software designed to enable researchers interested in roots
        by providing an easy-To-use interface, fast image processing and reliable
        measurements. The default broken roots mode is intended for roots sampled
        from pots and soil cores, washed and typically scanned on a flatbed scanner,
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        root mode for complete root systems or root crowns provides additional measurements
        such as angles, root depth and convex hull. Both modes support providing measurements
        grouped by defined diameter ranges, the inclusion of multiple regions of interest
        and batch analysis. RhizoVision Explorer was successfully validated against
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        that WinRhizo™ substantially underestimated root volume relative to RhizoVision
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        for collaborative improvement and reliable access to all.
      authors:
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      - name: Dhakal K.
      - name: Griffiths M.
      - name: Guo H.
      - name: Freschet G.T.
      - name: York L.M.
      citationCount: 130
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      journal: AoB PLANTS
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    note: null
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  - term: Plant biology
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  description: Freezing-Point is a user-friendly open-source software for the automated
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    url: https://github.com/reuter-group/webnma3
  - note: Helpdesk and support for ELIXIR Norway services.
    type:
    - Helpdesk
    url: https://elixir.no/helpdesk
  maturity: Mature
  name: WEBnma
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: UiB
  publication:
  - doi: 10.1186/s12859-014-0427-6
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) using elastic network models
        is a reliable and cost-effective computational method to characterise protein
        flexibility and by extension, their dynamics. Further insight into the dynamics-function
        relationship can be gained by comparing protein motions between protein homologs
        and functional classifications. This can be achieved by comparing normal modes
        obtained from sets of evolutionary related proteins. Results: We have developed
        an automated tool for comparative NMA of a set of pre-aligned protein structures.
        The user can submit a sequence alignment in the FASTA format and the corresponding
        coordinate files in the Protein Data Bank (PDB) format. The computed normalised
        squared atomic fluctuations and atomic deformation energies of the submitted
        structures can be easily compared on graphs provided by the web user interface.
        The web server provides pairwise comparison of the dynamics of all proteins
        included in the submitted set using two measures: the Root Mean Squared Inner
        Product and the Bhattacharyya Coefficient. The Comparative Analysis has been
        implemented on our web server for NMA, WEBnmat, which also provides recently
        upgraded functionality for NMA of single protein structures. This includes
        new visualisations of protein motion, visualisation of inter-residue correlations
        and the analysis of conformational change using the. In addition, programmatic
        access to WEBnmat is now available through a SOAP-based web service. WEBnmat
        is available at. Conclusion: WEBnmat v2.0 is an online tool offering unique
        capability for comparative NMA on multiple protein structures. Along with
        a convenient web interface, powerful computing resources, and several methods
        for mode analyses, WEBnmat facilitates the assessment of protein flexibility
        within protein families and superfamilies. These analyses can give a good
        view of how the structures move and how the flexibility is conserved over
        the different structures.'
      authors:
      - name: Tiwari S.P.
      - name: Fuglebakk E.
      - name: Hollup S.M.
      - name: Skjaerven L.
      - name: Cragnolini T.
      - name: Grindhaug S.H.
      - name: Tekle K.M.
      - name: Reuter N.
      citationCount: 87
      date: '2014-12-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnmat v2.0: Web server and services for comparing protein flexibility'
    note: null
    pmcid: PMC4339738
    pmid: '25547242'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1186/1471-2105-6-52
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) has become the method of choice
        to investigate the slowest motions in macromolecular systems. NMA is especially
        useful for large biomolecular assemblies, such as transmembrane channels or
        virus capsids. NMA relies on the hypothesis that the vibrational normal modes
        having the lowest frequencies (also named soft modes) describe the largest
        movements in a protein and are the ones that are functionally relevant. Results:
        We developed a web-based server to perform normal modes calculations and different
        types of analyses. Starting from a structure file provided by the user in
        the PDB format, the server calculates the normal modes and subsequently offers
        the user a series of automated calculations; normalized squared atomic displacements,
        vector field representation and animation of the first six vibrational modes.
        Each analysis is performed independently from the others and results can be
        visualized using only a web browser. No additional plug-in or software is
        required. For users who would like to analyze the results with their favorite
        software, raw results can also be downloaded. The application is available
        on http://www.bioinfo.no/tools/normalmodes. We present here the underlying
        theory, the application architecture and an illustration of its features using
        a large transmembrane protein as an example. Conclusion: We built an efficient
        and modular web application for normal mode analysis of proteins. Non specialists
        can easily and rapidly evaluate the degree of flexibility of multi-domain
        protein assemblies and characterize the large amplitude movements of their
        domains. © 2005 Hollup et al; licensee BioMed Central Ltd.'
      authors:
      - name: Hollup S.M.
      - name: Salensminde G.
      - name: Reuter N.
      citationCount: 105
      date: '2005-03-11T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnm@: A web application for normal mode analyses of proteins'
    note: null
    pmcid: PMC1274249
    pmid: '15762993'
    type:
    - Primary
    version: '1.0'
  relation:
  - biotoolsID: numpy
    type: uses
  - biotoolsID: biopython
    type: uses
  - biotoolsID: matplotlib
    type: uses
  - biotoolsID: mustang
    type: uses
  - biotoolsID: dssp
    type: uses
  toolType:
  - Web API
  - Suite
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  validated: 1
  version:
  - '3.5'
- accessibility: null
  additionDate: '2019-09-27T09:58:46Z'
  biotoolsCURIE: biotools:BioMercator
  biotoolsID: BioMercator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: BioMercator is a software that provides a complete set of algorithms
    and visualization tool covering all steps required to perform QTL meta-analysis,
    graphical representation of large datasets. User may import sequence and genome
    annotations datasets within the software in order to display functional annotation
    related to QTL and meta-QTL.
  documentation: []
  download:
  - note: null
    type: Binaries
    url: https://sourcesup.renater.fr/frs/?group_id=2301
    version: 4.2.3
  editPermission:
    authors:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: QTL map
        uri: http://edamontology.org/data_1860
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Genome map
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      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
    note: null
    operation:
    - term: Genetic mapping
      uri: http://edamontology.org/operation_0282
    - term: Physical mapping
      uri: http://edamontology.org/operation_2944
    output: []
  homepage: https://sourcesup.renater.fr/projects/biomercator
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-03-11T08:56:54.859634Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: BioMercator
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: admin
  publication:
  - doi: 10.1093/bioinformatics/bth230
    metadata:
      abstract: 'Summary: Breeding programs face the challenge of integrating information
        from genomics and from quantitative trait loci (QTL) analysis in order to
        identify genomic sequences controlling the variation of important traits.
        Despite the development of integrative databases, building a consensus map
        of genes, QTL and other loci gathered from multiple maps remains a manual
        and tedious task. Nevertheless, this is a critical step to reveal co-locations
        between genes and QTL. Another important matter is to determine whether QTL
        linked to same traits or related ones is detected in independent experiments
        and located in the same region, and represents a single locus or not. Statistical
        tools such as meta-analysis can be used to answer this question. BioMercator
        has been developed to automate map compilation and QTL meta-analysis, and
        to visualize co-locations between genes and QTL through a graphical interface.
        © Oxford University Press 2004; all rights reserved.'
      authors:
      - name: Arcade A.
      - name: Labourdette A.
      - name: Falque M.
      - name: Mangin B.
      - name: Chardon F.
      - name: Charcosset A.
      - name: Joets J.
      citationCount: 382
      date: '2004-09-22T00:00:00Z'
      journal: Bioinformatics
      title: 'BioMercator: Integrating genetic maps and QTL towards discovery of candidate
        genes'
    note: null
    pmcid: null
    pmid: '15059820'
    type: []
    version: '3'
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Quantitative genetics
    uri: http://edamontology.org/topic_3055
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  validated: 1
  version:
  - 4.2.3
- accessibility: null
  additionDate: '2023-05-22T15:10:32.141196Z'
  biotoolsCURIE: biotools:bigseqkit
  biotoolsID: bigseqkit
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: The Next Generation Sequencing (NGS) raw data are stored in FASTA and
    FASTQ text-based file formats. Common operations on FASTA/Q files include searching,
    filtering, sampling, deduplication and sorting, among others. We can find several
    tools in the literature for FASTA/Q file manipulation but none of them are well
    fitted for large files of tens of GB (likely TBs in the near future) since mostly
    they are based on sequential processing. The exception is seqkit that allows some
    routines to use a few threads but, in any case, the scalability is very limited.
    To deal with this issue, we introduce BigSeqKit, a parallel toolkit to manipulate
    FASTA/Q files at scale with speed and scalability at its core. BigSeqKit takes
    advantage of an HPC-Big Data framework (IgnisHPC) to parallelize and optimize
    the commands included in seqkit. In this way, in most cases it is from tens to
    hundreds of times faster than other state-of-the-art tools such as seqkit, samtools
    and pyfastx.
  documentation: []
  download: []
  editPermission:
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    - term: DNA transcription
      uri: http://edamontology.org/operation_0372
    - term: DNA translation
      uri: http://edamontology.org/operation_0371
    - term: Sequence conversion
      uri: http://edamontology.org/operation_0233
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/citiususc/BigSeqKit
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-01T11:28:15.208151Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: BigSeqKit
  operatingSystem:
  - Linux
  otherID: []
  owner: cesarpomar
  publication: []
  relation: []
  toolType:
  - Library
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2021-05-06T06:18:52Z'
  biotoolsCURIE: biotools:pangenome-blast
  biotoolsID: pangenome-blast
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Bielefeld University
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uni-bielefeld.de/
  - email: null
    fundrefid: null
    gridid: null
    name: Genome Informatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://gi.cebitec.uni-bielefeld.de/
  - email: plast-service@cebitec.uni-bielefeld.de
    fundrefid: null
    gridid: null
    name: Tizian Schulz
    note: null
    orcidid: https://orcid.org/0000-0003-0744-7078
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: PLAST is a heuristical method to search for highest scoring local alignments
    between a DNA sequence query and a graphical pangenome. It takes as input a plain
    DNA sequence and a pangenome which may either be a set of (multiple) FASTA or
    FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs
    statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard
    output format. Alignments are calculated based on a "seed-and-extend approach"
    while traversing the sequence graph. Biologically meaningful alignments are filtered
    by using an alignment statistic explicitly developed for sequence-to-graph alignments
    involving graphical pangenomes.
  documentation:
  - note: null
    type:
    - General
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.md
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLine
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: unambiguous pure nucleotide
        uri: http://edamontology.org/format_1211
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
    note: "In order to search for alignments within the pangenome graph, \nA pangenome\
      \ graph used to search for alignments consists of (1) a file in GFA format containing\
      \ all sequences of the graph, (2) a binary file produced by the tool itself\
      \ or the software \"Bifrost\" and (3) a program-specific index data structure\
      \ in binary format."
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BLAST results
        uri: http://edamontology.org/format_1333
  - cmd: PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fasta
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ
      files are not needed.
    operation:
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
  homepage: https://github.com/tischulz1/plast
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-26T11:22:02.485629Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast
  - note: null
    type:
    - Mirror
    url: https://github.com/tischulz1/plast
  maturity: Mature
  name: PLAST
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: tizian
  publication:
  - doi: 10.1093/bioinformatics/btab077
    metadata:
      abstract: 'Motivation: Increasing amounts of individual genomes sequenced per
        species motivate the usage of pangenomic approaches. Pangenomes may be represented
        as graphical structures, e.g. compacted colored de Bruijn graphs, which offer
        a low memory usage and facilitate reference-free sequence comparisons. While
        sequence-to-graph mapping to graphical pangenomes has been studied for some
        time, no local alignment search tool in the vein of BLAST has been proposed
        yet. Results: We present a new heuristic method to find maximum scoring local
        alignments of a DNA query sequence to a pangenome represented as a compacted
        colored de Bruijn graph. Our approach additionally allows a comparison of
        similarity among sequences within the pangenome. We show that local alignment
        scores follow an exponential-tail distribution similar to BLAST scores, and
        we discuss how to estimate its parameters to separate local alignments representing
        sequence homology from spurious findings. An implementation of our method
        is presented, and its performance and usability are shown. Our approach scales
        sublinearly in running time and memory usage with respect to the number of
        genomes under consideration. This is an advantage over classical methods that
        do not make use of sequence similarity within the pangenome.'
      authors:
      - name: Schulz T.
      - name: Wittler R.
      - name: Rahmann S.
      - name: Hach F.
      - name: Stoye J.
      citationCount: 6
      date: '2021-08-15T00:00:00Z'
      journal: Bioinformatics
      title: Detecting high-scoring local alignments in pangenome graphs
    note: null
    pmcid: PMC8388040
    pmid: '33532821'
    type:
    - Primary
    - Method
    - Benchmarking study
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 0.0.1-0.2.0
- accessibility: null
  additionDate: '2017-01-17T14:50:59Z'
  biotoolsCURIE: biotools:esiprot
  biotoolsID: esiprot
  collectionID:
  - ms-utils
  - Proteomics
  confidence_flag: null
  cost: null
  credit:
  - email: robert.winkler@ira.cinvestav.mx
    fundrefid: null
    gridid: null
    name: Robert Winkler
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Maintainer
    url: null
  - email: webmaster@ms-utils.org
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Documentor
    url: http://ms-utils.org
  description: Charge state determination and molecular weight calculation for low
    resolution electrospray ionization data.
  documentation:
  - note: null
    type:
    - General
    url: http://www.lababi.bioprocess.org/index.php/lababi-software/84-esiprot
  download:
  - note: null
    type: Source code
    url: http://www.bioprocess.org/esiprot/esiprot.zip
    version: null
  - note: null
    type: Source code
    url: http://www.bioprocess.org/esiprot/esiprot.zip
    version: null
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Peptide mass fingerprint
        uri: http://edamontology.org/data_0944
      format:
      - term: Mass spectrometry data format
        uri: http://edamontology.org/format_3245
    note: null
    operation:
    - term: Protein molecular weight calculation
      uri: http://edamontology.org/operation_0398
    - term: Protein fragment weight comparison
      uri: http://edamontology.org/operation_2929
    - term: Deisotoping
      uri: http://edamontology.org/operation_3629
    output:
    - data:
        term: Peptide mass fingerprint
        uri: http://edamontology.org/data_0944
      format:
      - term: Mass spectrometry data format
        uri: http://edamontology.org/format_3245
  homepage: https://nube-gran.de/esiprot
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-24T10:43:29.547210Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Mirror
    url: http://www.bioprocess.org/esiprot/esiprot_form.php
  - note: null
    type:
    - Software catalogue
    url: http://ms-utils.org
  maturity: null
  name: ESIprot
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: msutils_import
  publication:
  - doi: 10.1002/rcm.4384
    metadata:
      abstract: Electrospray ionization (ESI) ion trap mass spectrometers with relatively
        low resolution are frequently used for the analysis of natural products and
        peptides. Although ESI spectra of multiply charged protein molecules also
        can be measured on this type of devices, only average spectra are produced
        for the majority of naturally occurring proteins. Evaluating such ESI protein
        spectra would provide valuable information about the native state of investigated
        proteins. However, no suitable and freely available software could be found
        which allows the charge state determination and molecular weight calculation
        of single proteins from average ESI-MS data. Therefore, an algorithm based
        on standard deviation optimization (scatter minimization) was implemented
        for the analysis of protein ESI-MS data. The resulting software ESIprot was
        tested with ESI-MS data of six intact reference proteins between 12.4 and
        66.7kDa. In all cases, the correct charge states could be determined. The
        obtained absolute mass errors were in a range between -0.2 and 1.2Da, the
        relative errors below 30ppm. The possible mass accuracy allows for valid conclusions
        about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates
        an extraordinary robustness and allows spectral interpretation from as little
        as two peaks, given sufficient quality of the provided m/z data, without the
        necessity for peak intensity data. ESIprot is independent from the raw data
        format and the computer platform, making it a versatile tool for mass spectrometrists.
        The program code was released under the open-source GPLv3 license to support
        future developments of mass spectrometry software. © 2010 John Wiley & Sons,
        Ltd.
      authors:
      - name: Winkler R.
      citationCount: 75
      date: '2010-01-01T00:00:00Z'
      journal: Rapid Communications in Mass Spectrometry
      title: 'ESIprot: A universal tool for charge state determination and molecular
        weight calculation of proteins from electrospray ionization mass spectrometry
        data'
    note: null
    pmcid: null
    pmid: '20049890'
    type: []
    version: null
  relation: []
  toolType:
  - Web application
  - Desktop application
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  validated: 1
  version: []
- accessibility: null
  additionDate: '2026-02-22T16:52:58.409691Z'
  biotoolsCURIE: biotools:kollar
  biotoolsID: kollar
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: johan.lundin.kleberg@su.se
    fundrefid: null
    gridid: null
    name: Johan Lundin Kleberg
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: kollaR is an open-source R library for eye-tracking analysis and visualization,
    offering functions for event detection, AOI-based analyses, and algorithm comparison.  It
    provides implementations of several algorithms and includes visualizations for
    data exploration.
  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: Validation
      uri: http://edamontology.org/operation_2428
    - term: Clustering
      uri: http://edamontology.org/operation_3432
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  homepage: https://CRAN.R-project.org/package=kollaR
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-02-22T16:52:58.411587Z'
  license: GPL-3.0
  link: []
  maturity: null
  name: kollaR
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.3758/S13428-025-02903-Z
    metadata: null
    note: null
    pmcid: PMC12685970
    pmid: '41361102'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Imaging
    uri: http://edamontology.org/topic_3382
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Human biology
    uri: http://edamontology.org/topic_2815
  validated: 0
  version: []
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