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  description: Differential quantification of alternative splicing events on spliced
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  license: GPL-3.0
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  toolType:
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  description: Data analysis in the life sciences often suffers from reproducibility,
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    with scalability issues, limited portability due to tight coupling with the execution
    environment and accessibility constraints arising from the absence of user-friendly
    interfaces. To overcome these issues, we created CloWM, a comprehensive cloud-based
    workflow management platform that allows the generic transformation of command-line
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  topic:
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  validated: 0
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  description: Stressful experiences can induce maladaptive brain responses through
    gene expression changes, contributing to disorders such as depression and anxiety.
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    computational workflow to ensure comparability. Results are integrated in the
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  - term: Data visualisation
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  additionDate: '2026-01-30T11:47:35.909206Z'
  biotoolsCURIE: biotools:cineca-hpc
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    fundrefid: null
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    first-served). Projects involving non-sensitive data are unlimited and may be
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  documentation:
  - note: null
    type:
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  maturity: Legacy
  name: ELIXIR-CINECA-HPC
  operatingSystem:
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  publication:
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    metadata: null
    note: null
    pmcid: PMC7446135
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  - doi: 10.1186/s40537-024-01047-9
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    type:
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  relation:
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    type: uses
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    type: uses
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    type: uses
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  - biotoolsID: R
    type: uses
  - biotoolsID: biopython
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  - biotoolsID: hpc-reditools
    type: uses
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    type: uses
  - biotoolsID: tabix
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  - biotoolsID: cutadapt
    type: uses
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    type: uses
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    type: uses
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  - biotoolsID: star
    type: uses
  - biotoolsID: vcftools
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  toolType:
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  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2015-02-05T13:59:31Z'
  biotoolsCURIE: biotools:itsonedb
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  description: A comprehensive collection of the fungal ribosomal RNA Internal Transcribed
    Spacer 1 (ITS1) sequences aimed at supporting metagenomic surveys of fungal environmental
    communities.
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  function:
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    input: []
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    operation:
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  lastUpdate: '2026-01-30T10:26:56.768452Z'
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  name: ITSoneDB
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  biotoolsCURIE: biotools:unexakorea_dataset
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  confidence_flag: null
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  description: 'This Investigationevaluated the in vivo maintenance effect of a sustained-release
    vitamin formulation developed using the proprietary coating technology of unexakorea
    Inc. In a mouse model, the formulation demonstrated a stable plasma concentration
    for approximately 10–12 hours after administration.

    These findings suggest that the sustained-release formulation may serve as a promising
    alternative

    to conventional high-absorption formulations, offering improved physiological
    stability and reduced

    adverse effects associated with excessive absorption


    sustained-release, plasma concentration, Lipid Encapsulation Material'
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  license: null
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  name: unexakorea dataset
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  owner: unexakorea
  publication:
  - doi: 10.26434/chemrxiv-2025-2jq7b
    metadata: null
    note: Optimizing Pharmacokinetic Persistence of Functional Agents Through Next-Generation
      Sustained-Release Formulations
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: v1
  relation: []
  toolType: []
  topic:
  - term: Bioengineering
    uri: http://edamontology.org/topic_3398
  - term: Chemical biology
    uri: http://edamontology.org/topic_3369
  validated: 0
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    - Other
    url: https://summarized.science/about
  - note: FAQ page for the project
    type:
    - FAQ
    url: https://summarized.science/faq
  download: []
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  homepage: https://summarized.science/
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  license: null
  link:
  - note: GDPR complient newsletter
    type:
    - Mailing list
    url: https://summarized.science/#newsletter
  maturity: Mature
  name: summarized.science
  operatingSystem: []
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  owner: sybren
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version:
  - '1.1'
- accessibility: null
  additionDate: '2021-01-18T12:30:59Z'
  biotoolsCURIE: biotools:macse
  biotoolsID: macse
  collectionID: []
  confidence_flag: tool
  cost: null
  credit:
  - email: ranwez@supagro.fr
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
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    url: null
  description: 'Aligning Protein-Coding Nucleotide Sequences with MACSE.


    MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop
    Codons.


    A wide range of molecular analyses relies on multiple sequence alignments (MSA).


    MACSE aligns coding NT sequences with respect to their AA translation while allowing
    NT sequences to contain multiple frameshifts and or stop codons.'
  documentation: []
  download:
  - note: Pipelines source code
    type: Source code
    url: https://github.com/ranwez/MACSE_V2_PIPELINES
    version: null
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  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Global alignment
      uri: http://edamontology.org/operation_0496
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    - term: Frameshift detection
      uri: http://edamontology.org/operation_0265
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    output: []
  homepage: https://bioweb.supagro.inra.fr/macse/
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T16:37:52.513457Z'
  license: null
  link: []
  maturity: null
  name: MACSE
  operatingSystem: []
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  owner: Niclaskn
  publication:
  - doi: 10.1007/978-1-0716-1036-7_4
    metadata:
      abstract: '© 2021, Springer Science+Business Media, LLC, part of Springer Nature.Most
        genomic and evolutionary comparative analyses rely on accurate multiple sequence
        alignments. With their underlying codon structure, protein-coding nucleotide
        sequences pose a specific challenge for multiple sequence alignment. Multiple
        Alignment of Coding Sequences (MACSE) is a multiple sequence alignment program
        that provided the first automatic solution for aligning protein-coding gene
        datasets containing both functional and nonfunctional sequences (pseudogenes).
        Through its unique features, reliable codon alignments can be built in the
        presence of frameshifts and stop codons suitable for subsequent analysis of
        selection based on the ratio of nonsynonymous to synonymous substitutions.
        Here we offer a practical overview and guidelines on the use of MACSE v2.
        This major update of the initial algorithm now comes with a graphical interface
        providing user-friendly access to different subprograms to handle multiple
        alignments of protein-coding sequences. We also present new pipelines based
        on MACSE v2 subprograms to handle large datasets and distributed as Singularity
        containers. MACSE and associated pipelines are available at: https://bioweb.supagro.inra.fr/macse/.'
      authors:
      - name: Ranwez V.
      - name: Chantret N.
      - name: Delsuc F.
      citationCount: 1
      date: '2021-01-01T00:00:00Z'
      journal: Methods in Molecular Biology
      title: Aligning Protein-Coding Nucleotide Sequences with MACSE
    note: null
    pmcid: null
    pmid: '33289886'
    type: []
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Molecular evolution
    uri: http://edamontology.org/topic_3945
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:57.156578Z'
  biotoolsCURIE: biotools:incremental_naive_bayes_classifier
  biotoolsID: incremental_naive_bayes_classifier
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: gail.l.rosen@drexel.edu
    fundrefid: null
    gridid: null
    name: Gail L Rosen
    note: null
    orcidid: https://orcid.org/0000-0003-1763-5750
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: NBC++ is an incremental Naive Bayes classifier designed for metagenomic
    taxonomic classification. It focuses on query performance and memory efficiency,
    utilizing canonical k-mer storage and adaptable memory allocation, and is available
    through GitHub with a Dockerfile for easy deployment.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    output: []
  homepage: http://github.com/EESI/Naive_Bayes
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:22:57.158765Z'
  license: null
  link: []
  maturity: null
  name: NBC++ (Incremental Naive Bayes Classifier)
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTAE743
    metadata: null
    note: null
    pmcid: PMC11729721
    pmid: '39700412'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Database management
    uri: http://edamontology.org/topic_3489
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:56.131018Z'
  biotoolsCURIE: biotools:paired_disco_variants_consistently_matches
  biotoolsID: paired_disco_variants_consistently_matches
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: shams_bayzid@cse.buet.ac.bd
    fundrefid: null
    gridid: null
    name: Md Shamsuzzoha Bayzid
    note: null
    orcidid: https://orcid.org/0000-0002-5640-0615
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: DISCO-variants is a tool that improves phylogenomic analyses by decomposing
    multi-copy gene trees into single-copy trees. It introduces DISCO-R, a refined
    variant, and demonstrates improved accuracy compared to other methods like ASTRAL-Pro,
    especially when dealing with paralogs.
  documentation: []
  download: []
  editPermission:
    authors: []
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Tree dating
      uri: http://edamontology.org/operation_3942
    - term: Gene tree construction
      uri: http://edamontology.org/operation_0553
    - term: Phylogenetic tree reconciliation
      uri: http://edamontology.org/operation_3947
    output: []
  homepage: https://github.com/skhakim/DISCO-variants
  homepage_status: 0
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  lastUpdate: '2026-01-15T12:22:56.133283Z'
  license: null
  link: []
  maturity: null
  name: DISCO-variants
  operatingSystem: []
  otherID: []
  owner: pub2tools2024
  publication:
  - doi: 10.1093/BIOADV/VBAE189
    metadata: null
    note: null
    pmcid: PMC11634537
    pmid: '39664861'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-01-15T12:22:55.142660Z'
  biotoolsCURIE: biotools:adjusting_allele_frequencies_afs
  biotoolsID: adjusting_allele_frequencies_afs
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
  - email: leed13@miamioh.edu
    fundrefid: null
    gridid: null
    name: Donghyung Lee
    note: null
    orcidid: https://orcid.org/0000-0002-5145-3806
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: ZMIX is a software tool for estimating ancestry proportions in genome-wide
    association studies (GWAS) using only association Z-scores. It offers a novel
    method to overcome the challenge of inaccessible study reference allele frequencies.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Essential dynamics
      uri: http://edamontology.org/operation_3891
    - term: Variant prioritisation
      uri: http://edamontology.org/operation_3226
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    - term: Imputation
      uri: http://edamontology.org/operation_3557
    - term: Regression analysis
      uri: http://edamontology.org/operation_3659
    output: []
  homepage: https://github.com/statsleelab/gauss
  homepage_status: 0
  language: []
  lastUpdate: '2026-01-15T12:22:55.144594Z'
  license: null
  link: []
  maturity: null
  name: ZMIX
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  owner: pub2tools2024
  publication:
  - doi: 10.1093/BIOADV/VBAE128
    metadata: null
    note: null
    pmcid: PMC11632184
    pmid: '39664860'
    type: []
    version: null
  relation: []
  toolType: []
  topic:
  - term: GWAS study
    uri: http://edamontology.org/topic_3517
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  validated: 0
  version: []
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