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  - email: null
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    name: Andrew J Page
    note: null
    orcidid: null
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  description: Pairwise SNP distance matrix from a FASTA sequence alignment
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  language:
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  - Shell
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  owner: Pub2Tools
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  toolType:
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  topic:
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  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
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  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
    fundrefid: null
    gridid: null
    name: Simon E. Haendeler
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    rorid: null
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    url: null
  - email: null
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    rorid: null
    typeEntity: Person
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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:
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    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
  - note: Local source-checkout setup instructions.
    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:
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    type: Source code
    url: https://github.com/enesBerkSakalli/phylo-movies
    version: 0.98.1
  - note: Desktop convenience builds for macOS, Windows, and Linux.
    type: Binaries
    url: https://github.com/enesBerkSakalli/phylo-movies/releases/tag/v0.98.1
    version: 0.98.1
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  function:
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    input:
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    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Visualizes ordered phylogenetic tree series as animated transition movies
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    operation:
    - term: Phylogenetic tree visualisation
      uri: http://edamontology.org/operation_0567
    - term: Phylogenetic tree analysis
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    - data:
        term: Phylogenetic tree
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      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://enesberksakalli.github.io/phylo-movies/
  homepage_status: 0
  language:
  - Python
  - 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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  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:
    - Primary
    version: 0.98.1
  relation: []
  toolType:
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  - Web application
  topic:
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 0
  version:
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- accessibility: null
  additionDate: '2026-06-12T12:09:48.272845Z'
  biotoolsCURIE: biotools:nallo
  biotoolsID: nallo
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
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    fundrefid: null
    gridid: null
    name: Lars Feuk
    note: null
    orcidid: https://orcid.org/0000-0003-2355-2919
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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.'
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      - term: BAI
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  language:
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  - Java
  lastUpdate: '2026-06-12T14:03:07.797466Z'
  license: MIT
  link:
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    url: https://github.com/genomic-medicine-sweden/nallo
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  publication:
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    metadata: null
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    pmcid: PMC12988770
    pmid: '41712762'
    type: []
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  toolType: []
  topic:
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  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Whole genome sequencing
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  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Epigenetics
    uri: http://edamontology.org/topic_3295
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2026-06-10T15:44:24.553891Z'
  biotoolsCURIE: biotools:flavotyper
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  description: FlavoTyper is a bioinformatics tool that performs in silico serotyping
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  documentation:
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    note: null
    operation:
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  language:
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  lastUpdate: '2026-06-10T17:14:53.654094Z'
  license: Apache-2.0
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  maturity: Emerging
  name: FlavoTyper
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  owner: Salmam2
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  toolType:
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  - Web service
  topic:
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Veterinary medicine
    uri: http://edamontology.org/topic_3397
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-06-04T08:25:03.738887Z'
  biotoolsCURIE: biotools:VerityMap
  biotoolsID: VerityMap
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  description: VerityMap is a tool for mapping long reads to assemblies of extra-long
    tandem repeats, producing SAM files and identifying potential heterozygous sites
    and assembly errors through analysis of rare k-mers. It supports PacBio HiFi and
    ONT reads and generates interactive HTML plots for variant analysis.
  documentation: []
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    note: null
    operation:
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      format:
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      - term: BED
        uri: http://edamontology.org/format_3003
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  homepage_status: 0
  language:
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  - CUDA
  - Python
  - C++
  lastUpdate: '2026-06-04T08:25:03.740814Z'
  license: GPL-3.0
  link:
  - note: null
    type:
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    url: https://github.com/ablab/tandemQUAST/issues
  maturity: Mature
  name: VerityMap
  operatingSystem: []
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  owner: n.m.palmblad@lumc.nl
  publication:
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    metadata: null
    note: null
    pmcid: PMC7355294
    pmid: '32657355'
    type: []
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  topic:
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  - term: Genomics
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  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-06-04T08:08:16.771951Z'
  biotoolsCURIE: biotools:screen_assembly
  biotoolsID: screen_assembly
  collectionID: []
  confidence_flag: null
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    note: null
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    rorid: null
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  description: 'Screen a bacterial assembly (contigs/CDS or proteins) for nucleotide
    or protein sequences.


    Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies.
    Generates multiple CSVs and plots that describe which genes are present and how
    variable their sequence is. Can use DNA or protein query sequences (GOIs) and
    DNA contigs/fastas or protein fastas as database (db) to search in.'
  documentation:
  - note: null
    type:
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    url: https://github.com/shimbalama/screen_assembly/wiki
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  function:
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    input:
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      format:
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    note: null
    operation:
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format: []
    - data:
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      format: []
  homepage: https://github.com/shimbalama/screen_assembly
  homepage_status: 0
  language:
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  lastUpdate: '2026-06-04T08:08:16.774426Z'
  license: MIT
  link:
  - note: null
    type:
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    url: https://github.com/shimbalama/screen_assembly
  maturity: Mature
  name: screen_assembly
  operatingSystem: []
  otherID: []
  owner: aniehues
  publication:
  - doi: 10.1038/s41588-019-0417-8
    metadata: null
    note: null
    pmcid: PMC6650292
    pmid: '31133745'
    type:
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    version: null
  relation: []
  toolType:
  - Script
  - Command-line tool
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version:
  - v1
- accessibility: null
  additionDate: '2026-06-04T07:54:19.689100Z'
  biotoolsCURIE: biotools:LongTR
  biotoolsID: LongTR
  collectionID: []
  confidence_flag: null
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  description: Tandem repeat genotyping with long reads, being a modified version
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  function:
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    input:
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    - data:
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      format:
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    note: null
    operation:
    - term: Genotyping
      uri: http://edamontology.org/operation_3196
    output:
    - data:
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  homepage: https://github.com/gymrek-lab/LongTR
  homepage_status: 0
  language:
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  - C
  - Shell
  lastUpdate: '2026-06-04T07:54:19.694217Z'
  license: GPL-2.0
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  otherID: []
  owner: veitveit11
  publication:
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    metadata: null
    note: null
    pmcid: PMC11229021
    pmid: '38965568'
    type: []
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  relation: []
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  topic:
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  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Long-read sequencing
    uri: http://edamontology.org/topic_4056
  validated: 0
  version:
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  additionDate: '2026-05-20T08:59:02.212508Z'
  biotoolsCURIE: biotools:snp-sites
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  description: Finds SNP sites from a multi-FASTA alignment file.
  documentation:
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  function:
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    note: null
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      format:
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  homepage_status: 0
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  owner: aniehues
  publication:
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  - note: null
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  description: shic is a collection of shims for use in automated workflow composition
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  biotoolsCURIE: biotools:pathotypr
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  description: 'A fast, offline, pathogen-agnostic toolkit for lineage classification
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    note: predict — Assign lineages to genomes using a pre-trained Random Forest model.
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  description: Functional cluster of MHC class I molecules (MHCI) based on their predicted
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      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: provides heat-map and graphical tree-based visualizations of the functional
      relationship between MHC class I and class II variants
    operation:
    - term: Functional clustering
      uri: http://edamontology.org/operation_3459
    output:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: Phylogenetic tree format
        uri: http://edamontology.org/format_2006
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
  homepage: http://cbs.dtu.dk/services/MHCcluster/
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-20T11:08:19.028012Z'
  license: Other
  link:
  - note: null
    type:
    - Software catalogue
    url: http://cbs.dtu.dk/services
  maturity: Emerging
  name: MHCcluster
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: liuyang
  publication:
  - doi: 10.1007/s00251-013-0714-9
    metadata:
      abstract: The identification of peptides binding to major histocompatibility
        complexes (MHC) is a critical step in the understanding of T cell immune responses.
        The human MHC genomic region (HLA) is extremely polymorphic comprising several
        thousand alleles, many encoding a distinct molecule. The potentially unique
        specificities remain experimentally uncharacterized for the vast majority
        of HLA molecules. Likewise, for nonhuman species, only a minor fraction of
        the known MHC molecules have been characterized. Here, we describe a tool,
        MHCcluster, to functionally cluster MHC molecules based on their predicted
        binding specificity. The method has a flexible web interface that allows the
        user to include any MHC of interest in the analysis. The output consists of
        a static heat map and graphical tree-based visualizations of the functional
        relationship between MHC variants and a dynamic TreeViewer interface where
        both the functional relationship and the individual binding specificities
        of MHC molecules are visualized. We demonstrate that conventional sequence-based
        clustering will fail to identify the functional relationship between molecules,
        when applied to MHC system, and only through the use of the predicted binding
        specificity can a correct clustering be found. Clustering of prevalent HLA-A
        and HLA-B alleles using MHCcluster confirms the presence of 12 major specificity
        groups (supertypes) some however with highly divergent specificities. Importantly,
        some HLA molecules are shown not to fit any supertype classification. Also,
        we use MHCcluster to show that chimpanzee MHC class I molecules have a reduced
        functional diversity compared to that of HLA class I molecules. MHCcluster
        is available at www.cbs.dtu.dk/services/MHCcluster-2.0. © 2013 Springer-Verlag
        Berlin Heidelberg.
      authors:
      - name: Thomsen M.
      - name: Lundegaard C.
      - name: Buus S.
      - name: Lund O.
      - name: Nielsen M.
      citationCount: 60
      date: '2013-09-01T00:00:00Z'
      journal: Immunogenetics
      title: MHCcluster, a method for functional clustering of MHC molecules
    note: null
    pmcid: PMC3750724
    pmid: '23775223'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Immunoproteins, genes and antigens
    uri: http://edamontology.org/topic_2830
  validated: 1
  version:
  - '2.0'
- accessibility: Open access
  additionDate: '2017-08-20T16:07:58Z'
  biotoolsCURIE: biotools:htslib
  biotoolsID: htslib
  collectionID:
  - Animal and Crop Genomics
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: The main purpose of HTSlib is to provide access to genomic information
    files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF
    and BCF formats). The library also provides interfaces to access and index genome
    reference data in FASTA format and tab-delimited files with genomic coordinates.
    It is utilized and incorporated into both SAMtools and BCFtools.
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
  editPermission:
    authors:
    - animalandcropgenomics
    - smoe
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-03-18T17:33:38.200309Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/htslib
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/htslib/issues
  maturity: Mature
  name: HTSlib
  operatingSystem:
  - Windows
  - Linux
  - Mac
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/gigascience/giab007
    metadata: null
    note: 'HTSlib: C library for reading/writing high-throughput sequencing data.'
    pmcid: PMC7931820
    pmid: '33594436'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: samtools
    type: usedBy
  - biotoolsID: bcftools
    type: usedBy
  toolType:
  - Library
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
  - '1.0'
  - '1.1'
  - '1.2'
  - 1.2.1
  - '1.3'
  - 1.3.1
  - 1.3.2
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
  - 1.21.1
  - '1.22'
  - 1.22.1
  - 1.22.2
  - '1.23'
  - 1.23.1
- accessibility: Open access
  additionDate: '2017-01-13T13:16:01Z'
  biotoolsCURIE: biotools:quast
  biotoolsID: quast
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: quast.support@cab.spbu.ru
    fundrefid: null
    gridid: null
    name: QUAST Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: "QUAST stands for QUality ASsessment Tool.  \nIt evaluates a quality\
    \ of genome assemblies by computing various metrics and providing nice reports."
  documentation:
  - note: null
    type:
    - General
    url: http://quast.bioinf.spbau.ru/
  download: []
  editPermission:
    authors:
    - ELIXIR-CZ
    - Keiler_Collier
    - rathor2611
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: quast -ek assembly.fa --out output_prefix
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: '# Running quast on a eukaryotic genome'
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output: []
  homepage: http://quast.sourceforge.net/quast
  homepage_status: 0
  language:
  - Perl
  - Python
  - C
  lastUpdate: '2026-03-13T09:39:06.494933Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/ablab/quast
  - note: null
    type:
    - Issue tracker
    url: https://github.com/ablab/quast/issues
  maturity: Mature
  name: QUAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1093/bioinformatics/btt086
    metadata:
      abstract: Limitations of genome sequencing techniques have led to dozens of
        assembly algorithms, none of which is perfect. A number of methods for comparing
        assemblers have been developed, but none is yet a recognized benchmark. Further,
        most existing methods for comparing assemblies are only applicable to new
        assemblies of finished genomes; the problem of evaluating assemblies of previously
        unsequenced species has not been adequately considered. Here, we present QUAST
        - a quality assessment tool for evaluating and comparing genome assemblies.
        This tool improves on leading assembly comparison software with new ideas
        and quality metrics. QUAST can evaluate assemblies both with a reference genome,
        as well as without a reference. QUAST produces many reports, summary tables
        and plots to help scientists in their research and in their publications.
        In this study, we used QUAST to compare several genome assemblers on three
        datasets. QUAST tables and plots for all of them are available in the Supplementary
        Material, and interactive versions of these reports are on the QUAST website.
        © 2013 The Author.
      authors:
      - name: Gurevich A.
      - name: Saveliev V.
      - name: Vyahhi N.
      - name: Tesler G.
      citationCount: 6872
      date: '2013-04-15T00:00:00Z'
      journal: Bioinformatics
      title: 'QUAST: Quality assessment tool for genome assemblies'
    note: null
    pmcid: PMC3624806
    pmid: '23422339'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - v.5.3.0
- accessibility: Open access
  additionDate: '2016-03-17T13:51:10Z'
  biotoolsCURIE: biotools:webnma
  biotoolsID: webnma
  collectionID:
  - BiB tools
  - CBU tools
  - UiB tools
  - ELIXIR-NO
  - ELIXIR-Norway
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: Nathalie.Reuter@uib.no
    fundrefid: null
    gridid: null
    name: Nathalie Reuter
    note: null
    orcidid: https://orcid.org/0000-0002-3649-7675
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: http://www.cbu.uib.no/reuter/
  - email: null
    fundrefid: null
    gridid: null
    name: Sandhya P Tiwari
    note: null
    orcidid: https://orcid.org/0000-0002-0747-3826
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kidane M Tekle
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Tristan Cragnolini
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Svenn H Grindhaug
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Lars Skjærven
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Gisle Salensminde
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Edvin Fuglebakk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Siv M Hollup
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Department of Molecular Biology, University of Bergen, Norway
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Computational Biology Unit, Department of Informatics, University of Bergen,
      Norway
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: UiB
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: WEBnm@ provides quick, automated computation and analysis of low-frequency
    normal modes for protein structures.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: http://apps.cbu.uib.no/webnma3/howto/single
  - note: null
    type:
    - FAQ
    url: http://apps.cbu.uib.no/webnma3/qanda
  - note: null
    type:
    - General
    - Citation instructions
    url: http://apps.cbu.uib.no/webnma3/about
  download: []
  editPermission:
    authors:
    - eca008
    - korbinib
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Norway
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Constructs elastic network model from alpha carbon coordinates of the protein,
      and computes properties to describe large scale conformations. Computes normal
      modes, fluctuation profiles, inter-residue correlations, conformational overlap
      analysis and vector field representations. Structural amino acid profiles, and
      normal mode characteristics describing protein motion, visualized in plots and
      decorated structure visualizations. White space delimited tabular data for normal
      modes and the provided plots
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Protein flexibility and motion analysis
      uri: http://edamontology.org/operation_0244
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Sequence profile
        uri: http://edamontology.org/data_1354
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Performs comparative analysis of the normal modes of protein structures.
      Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner
      Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins
      to be compared. Multiple protein structures Heatmaps, dendrograms and structural
      amino acid profiles for visual comparison of structural similarity. White space
      delimited tabular data for the provided plots
    operation:
    - term: Protein structure comparison
      uri: http://edamontology.org/operation_2487
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Structural profile
        uri: http://edamontology.org/data_0889
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://apps.cbu.uib.no/webnma
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-11T08:56:55.566213Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    - Issue tracker
    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: Open access
  additionDate: '2026-02-22T14:20:37.167505Z'
  biotoolsCURIE: biotools:mapler
  biotoolsID: mapler
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: nicolas.maurice@inria.fr
    fundrefid: null
    gridid: null
    name: Nicolas Maurice
    note: null
    orcidid: https://orcid.org/0009-0009-9615-2765
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Claire Lemaitre
    note: null
    orcidid: https://orcid.org/0000-0001-8675-170X
    rorid: null
    typeEntity: null
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Riccardo Vicedomini
    note: null
    orcidid: https://orcid.org/0000-0002-7706-0998
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: clemence.frioux@inria.fr
    fundrefid: null
    gridid: null
    name: Clémence Frioux
    note: null
    orcidid: https://orcid.org/0000-0003-2114-0697
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Mapler is a pipeline for assessing assembly quality in taxonomically
    rich metagenomes sequenced with HiFi reads. It incorporates state-of-the-art metrics
    and facilitates the comparison of assembly strategies.
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  download: []
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  function:
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    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
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        uri: http://edamontology.org/format_1929
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
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        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    - term: Sample comparison
      uri: http://edamontology.org/operation_3731
    output:
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Read binning
      uri: http://edamontology.org/operation_3798
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/Nimauric/Mapler
  homepage_status: 0
  language:
  - Bash
  - Python
  lastUpdate: '2026-03-10T15:44:03.311515Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/Nimauric/Mapler
  maturity: null
  name: Mapler
  operatingSystem: []
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  owner: nimauric
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTAF334
    metadata: null
    note: null
    pmcid: PMC12205171
    pmid: '40478660'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version: []
- accessibility: null
  additionDate: '2015-06-29T10:13:32Z'
  biotoolsCURIE: biotools:netphos
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  cost: Free of charge (with restrictions)
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    name: CBS
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.bioinformatics.dtu.dk/english/Service/Contact
  - email: nblom@kt.dtu.dk
    fundrefid: null
    gridid: null
    name: Nicolaj Blom
    note: null
    orcidid: http://orcid.org/0000-0001-7787-7853
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: Neural network predictions for serine, threonine and tyrosine phosphorylation
    sites in eukaryotic proteins.
  documentation:
  - note: null
    type:
    - General
    url: http://www.cbs.dtu.dk/services/NetPhos/instructions.php
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  function:
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    input:
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        term: Sequence
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        uri: http://edamontology.org/format_1929
    note: produces neural network predictions for serine, threonine and tyrosine phosphorylation
      sites in eukaryotic proteins
    operation:
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    output:
    - data:
        term: Protein features
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      format:
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    - data:
        term: Sequence report
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      format:
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        uri: http://edamontology.org/format_2333
  homepage: http://cbs.dtu.dk/services/NetPhos/
  homepage_status: 0
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  lastUpdate: '2026-03-05T12:16:41.386128Z'
  license: Other
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    type:
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  maturity: Emerging
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  publication:
  - doi: 10.1006/jmbi.1999.3310
    metadata:
      abstract: Protein phosphorylation at serine, threonine or tyrosine residues
        affects a multitude of cellular signaling processes. How is specificity in
        substrate recognition and phosphorylation by protein kinases achieved? Here,
        we present an artificial neural network method that predicts phosphorylation
        sites in independent sequences with a sensitivity in the range from 69% to
        96%. As an example, we predict novel phosphorylation sites in the p300/CBP
        protein that may regulate interaction with transcription factors and histone
        acetyltransferase activity. In addition, serine and threonine residues in
        p300/CBP that can be modified by O-linked glycosylation with N-acetylglucosamine
        are identified. Glycosylation may prevent phosphorplation at these sites,
        a mechanism named yin-yang regulation. The prediction server is available
        on the Internet at http://www.cbs.dtu.dk/services/NetPhos/or via e-mail to
        NetPhos@@@cbs.dtu.dk.
      authors:
      - name: Blom N.
      - name: Gammeltoft S.
      - name: Brunak S.
      citationCount: 2373
      date: '1999-12-17T00:00:00Z'
      journal: Journal of Molecular Biology
      title: Sequence and structure-based prediction of eukaryotic protein phosphorylation
        sites
    note: null
    pmcid: null
    pmid: '10600390'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Web application
  - Web service
  topic:
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version:
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- accessibility: null
  additionDate: '2023-05-22T15:10:32.141196Z'
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  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
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    and pyfastx.
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  function:
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    input:
    - data:
        term: DNA sequence
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      format:
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        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
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      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:
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    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: []
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  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:
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    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:
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- accessibility: Open access
  additionDate: '2016-12-19T14:29:34Z'
  biotoolsCURIE: biotools:cuffcompare
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    gridid: null
    name: Galaxy Support Team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: Compare assembled transcripts to a reference annotation and track Cufflinks
    transcripts across multiple experiments.
  documentation:
  - note: null
    type:
    - General
    url: http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/
  download: []
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  function:
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    input:
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      format:
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        uri: http://edamontology.org/format_1975
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        uri: http://edamontology.org/format_2306
    - data:
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      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
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      format:
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  homepage: http://cole-trapnell-lab.github.io/cufflinks/
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-26T11:14:58.790920Z'
  license: null
  link:
  - note: null
    type:
    - Galaxy service
    url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/cuffcompare/cuffcompare/2.2.1.0
  maturity: Mature
  name: cuffcompare
  operatingSystem:
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  otherID: []
  owner: hmenager
  publication:
  - doi: 10.1038/nbt.1621
    metadata: null
    note: null
    pmcid: PMC3146043
    pmid: '20436464'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkw343
    metadata: null
    note: null
    pmcid: PMC4987906
    pmid: '27137889'
    type:
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    version: null
  - doi: 10.7490/f1000research.1114334.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
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  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
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- accessibility: null
  additionDate: '2026-02-16T08:19:06.415244Z'
  biotoolsCURIE: biotools:fur
  biotoolsID: fur
  collectionID: []
  confidence_flag: null
  cost: null
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  description: The program fur takes as input a set of target genome sequences and
    a set of related genome sequences, the neighbors. It returns the sequence regions
    common to all targets that are absent form the neighbors. Such regions can be
    used as candidate genetic markers.
  documentation: []
  download: []
  editPermission:
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    type: public
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence record
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      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Nucleic acid comparison
      uri: http://edamontology.org/operation_2998
    output:
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        term: Nucleic acid sequence
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      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/evolbioinf/fur
  homepage_status: 0
  language:
  - Go
  lastUpdate: '2026-02-16T08:19:06.417279Z'
  license: null
  link: []
  maturity: null
  name: fur
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  owner: bebatut
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  relation: []
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  topic:
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    uri: http://edamontology.org/topic_3344
  validated: 0
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- accessibility: null
  additionDate: '2023-06-07T03:22:25.847061Z'
  biotoolsCURIE: biotools:metabuli
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  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'Metabuli: specific and sensitive metagenomic classification via joint
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  documentation: []
  download: []
  editPermission:
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  function:
  - cmd: null
    input:
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        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
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        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
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      format: []
  homepage: https://metabuli.steineggerlab.com
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-12T14:21:25.897853Z'
  license: GPL-3.0
  link:
  - note: null
    type:
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  maturity: Mature
  name: metabuli
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  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1038/s41592-024-02273-y
    metadata: null
    note: null
    pmcid: null
    pmid: '38769467'
    type: []
    version: null
  relation:
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    type: uses
  - biotoolsID: gtdb
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Data deposition
      uri: http://edamontology.org/operation_3431
    - term: Annotation
      uri: http://edamontology.org/operation_0226
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: FASTA-HTML
        uri: http://edamontology.org/format_2310
  homepage: https://globalamfungi.com/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2025-12-16T11:00:25.337448Z'
  license: CC-BY-4.0
  link:
  - note: null
    type:
    - Helpdesk
    - Repository
    - Service
    url: https://globalamfungi.com/
  maturity: Mature
  name: globalamfungi
  operatingSystem: []
  otherID: []
  owner: TomasVetrovsky
  publication:
  - doi: 10.1111/nph.19283
    metadata:
      abstract: null
      authors: []
      citationCount: 0
      date: null
      journal: null
      title: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  - Web application
  topic:
  - term: Biodiversity
    uri: http://edamontology.org/topic_3050
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2025-12-15T14:17:14.627791Z'
  biotoolsCURIE: biotools:asafind
  biotoolsID: asafind
  collectionID:
  - ELIXIR-CZ
  - Czech Republic
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: mvohnoutova@jcu.cz
    fundrefid: null
    gridid: null
    name: Marta Vohnoutová
    note: null
    orcidid: https://orcid.org/0000-0002-8915-8626
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    - Maintainer
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Vohnoutova_Marta_61699
  - email: agruber@prf.jcu.cz
    fundrefid: null
    gridid: null
    name: Ansgar Gruber
    note: null
    orcidid: https://orcid.org/0000-0002-5876-4391
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    url: https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gruber_Ansgar_118401
  description: "ASAFind is a software that predicts the intracellular location of\
    \ proteins in cells with four membrane-bound complex plastids of red algal origin.\
    \ \nThese plastids evolved via eukaryote-eukaryote endosymbiosis and for example\
    \ can be found in diatoms and cryptophytes. ASAFind uses protein sequence data\
    \ and external predictions of signal peptides (by the tools SignalP and TargetP),\
    \ and predicts plastid proteins, and proteins that are targeted to the periplastidic\
    \ compartment from these data; optionally, a graphical output can generated."
  documentation:
  - note: null
    type:
    - Installation instructions
    url: https://asafind.jcu.cz/download-page/
  download:
  - note: Download page on web-service, links to repository
    type: Downloads page
    url: https://asafind.jcu.cz/download-page/
    version: '2.0'
  editPermission:
    authors:
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    type: group
  elixirCommunity:
  - Plant Sciences
  - Marine Metagenomics
  - Microbial Biotechnology
  elixirNode:
  - Czech Republic
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format: []
    note: null
    operation:
    - term: Subcellular localisation prediction
      uri: http://edamontology.org/operation_2489
    - term: Sequence motif recognition
      uri: http://edamontology.org/operation_0239
    - term: Protein cleavage site prediction
      uri: http://edamontology.org/operation_0422
    output:
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format: []
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format: []
  homepage: https://asafind.jcu.cz/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-15T17:36:43.189214Z'
  license: CC-BY-SA-4.0
  link:
  - note: Web Service
    type:
    - Service
    url: https://asafind.jcu.cz
  - note: Information and source code, for local installation or development
    type:
    - Repository
    url: https://github.com/ASAFind/ASAFind-2
  maturity: Mature
  name: ASAFind
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: martavohnoutova
  publication:
  - doi: 10.1111/tpj.70138
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-06-01T00:00:00Z'
      journal: Plant Journal
      title: 'ASAFind 2.0: multi-class protein targeting prediction for diatoms and
        algae with complex plastids'
    note: Publication of the current version of ASAFind (2.0)
    pmcid: PMC12136025
    pmid: '40464854'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1111/tpj.12734
    metadata:
      abstract: ''
      authors: []
      citationCount: 138
      date: '2015-02-01T00:00:00Z'
      journal: Plant Journal
      title: Plastid proteome prediction for diatoms and other algae with secondary
        plastids of the red lineage
    note: Publication of the first version of ASAFind
    pmcid: PMC4329603
    pmid: '25438865'
    type:
    - Other
    version: '1.0'
  - doi: 10.48550/arXiv.2303.02509
    metadata: null
    note: Benchmarking of the performance of the first version of ASAFind
    pmcid: null
    pmid: null
    type:
    - Benchmarking study
    version: '1.0'
  relation:
  - biotoolsID: signalp
    type: uses
  - biotoolsID: targetp
    type: uses
  toolType:
  - Script
  - Command-line tool
  - Web service
  topic:
  - term: Cell biology
    uri: http://edamontology.org/topic_2229
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - '2.0'
- accessibility: Open access
  additionDate: '2022-04-19T09:32:41.303637Z'
  biotoolsCURIE: biotools:metagwgs
  biotoolsID: metagwgs
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: claire.hoede@inrae.fr
    fundrefid: null
    gridid: null
    name: Claire Hoede
    note: null
    orcidid: https://orcid.org/0000-0001-5054-7731
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: GenoToul bioinformatics facility
    note: null
    orcidid: null
    rorid: null
    typeEntity: Division
    typeRole:
    - Provider
    url: http://bioinfo.genotoul.fr/
  description: metagWGS is a workflow dedicated to the analysis of metagenomic data.
    It allows assembly, taxonomic annotation, and functional annotation of predicted
    genes. Since release 2.3, binning step with the possibility of cross-alignment
    is included. It has been developed in collaboration with several CATI BIOS4biol
    agents. Funded by Antiselfish Project (Labex Ecofect), ExpoMicoPig project (France
    Futur elevage) and SeqOccIn project (CPER - Occitanie Toulouse / FEDER), ATB_Biofilm
    funded by PNREST Anses, France genomique (ANR-10-INBS-09-08) and Resalab Ouest.
  documentation:
  - note: We provide up to date installation documentation, usage documentation, output
      description and functionnal test datasets and procedure.
    type:
    - User manual
    url: https://genotoul-bioinfo.pages-forge.inrae.fr/metagwgs/master/index.html
  download:
  - note: Functional tests data and script
    type: Test data
    url: https://forgemia.inra.fr/genotoul-bioinfo/metagwgs-test-datasets
    version: null
  editPermission:
    authors:
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    type: group
  elixirCommunity: []
  elixirNode:
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  elixirPlatform: []
  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
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
  - 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: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    output:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format:
      - term: Format
        uri: http://edamontology.org/format_1915
  - 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: De-novo assembly
      uri: http://edamontology.org/operation_0524
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://forgemia.inra.fr/genotoul-bioinfo/metagwgs
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-11T14:51:44.804907Z'
  license: GPL-3.0
  link:
  - note: See documentation, source code and functionnal test documentation.
    type:
    - Repository
    url: https://forge.inrae.fr/genotoul-bioinfo/metagwgs
  maturity: Mature
  name: metagWGS
  operatingSystem:
  - Linux
  otherID: []
  owner: choede
  publication: []
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  validated: 0
  version:
  - '2.3'
  - 2.5.0
- accessibility: Open access
  additionDate: '2019-02-13T17:01:40Z'
  biotoolsCURIE: biotools:Jalview
  biotoolsID: Jalview
  collectionID:
  - ELIXIR-UK
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Jim Procter
    note: null
    orcidid: https://orcid.org/0000-0002-7865-7382
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.lifesci.dundee.ac.uk/people/jim-procter
  - email: null
    fundrefid: null
    gridid: null
    name: Geoff Barton
    note: null
    orcidid: https://orcid.org/0000-0002-9014-5355
    rorid: null
    typeEntity: null
    typeRole: []
    url: https://www.lifesci.dundee.ac.uk/people/geoff-barton
  description: Jalview is a free cross-platform program for multiple sequence alignment
    editing, visualisation and analysis. Use it to align, view and edit sequence alignments,
    analyse them with phylogenetic trees and principal components analysis (PCA) plots
    and explore molecular structures and annotation.
  documentation:
  - note: null
    type:
    - Citation instructions
    url: https://www.jalview.org/about/citation
  - note: Hands-on exercises, Training courses and Training videos
    type:
    - Training material
    url: https://www.jalview.org/training/
  - note: null
    type:
    - FAQ
    url: https://www.jalview.org/help/faq
  - note: null
    type:
    - User manual
    url: https://www.jalview.org/help/documentation/
  download:
  - note: null
    type: Downloads page
    url: https://www.jalview.org/download
    version: null
  - note: null
    type: Source code
    url: https://www.jalview.org/download/source/
    version: null
  - note: Binaries for all platforms
    type: Binaries
    url: https://www.jalview.org/download/?os=all
    version: null
  - note: null
    type: Icon
    url: https://www.jalview.org/favicon.svg
    version: null
  - note: Executable JAR file
    type: Binaries
    url: https://www.jalview.org/download/other/jar/
    version: null
  editPermission:
    authors:
    - ben_s
    - jimprocter
    type: group
  elixirCommunity: []
  elixirNode:
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  elixirPlatform:
  - Tools
  - Interoperability
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: GFF2-seq
        uri: http://edamontology.org/format_1938
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: RNAML
        uri: http://edamontology.org/format_3311
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: mmCIF
        uri: http://edamontology.org/format_1477
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: VCF
        uri: http://edamontology.org/format_3016
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: 'Other Input formats:

      AMSA (.amsa);

      JnetFile (.concise, .jnet);

      PFAM (.pfam);

      Substitution matrix (.matrix);

      Jalview Project File (.jvp);

      Jalview Feature File (.features, .jvfeatures);

      Jalview Annotations File (.annotations, .jvannotations);

      Predicted Aligned Error (PAE) Matrix File (.json)

      ...

      Other Output formats:

      PFAM (.pfam);

      BioJS (.biojs) (interactive HTML/Javascript);

      Jalview Project File (.jvp);'
    operation:
    - term: Sequence alignment editing
      uri: http://edamontology.org/operation_3081
    - term: Phylogenetic tree analysis
      uri: http://edamontology.org/operation_0324
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: Pileup
        uri: http://edamontology.org/format_3015
      - term: BLC
        uri: http://edamontology.org/format_3313
      - term: BioJSON (Jalview)
        uri: http://edamontology.org/format_3774
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: JSON
        uri: http://edamontology.org/format_3464
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: GCG MSF
        uri: http://edamontology.org/format_1947
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: EPS
        uri: http://edamontology.org/format_3466
      - term: Format
        uri: http://edamontology.org/format_1915
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: SVG
        uri: http://edamontology.org/format_3604
      - term: PNG
        uri: http://edamontology.org/format_3603
  homepage: https://www.jalview.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-12-11T14:16:30.074724Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Discussion forum
    url: https://discourse.jalview.org/
  - note: null
    type:
    - Issue tracker
    url: https://issues.jalview.org/
  - note: Latest development version
    type:
    - Other
    url: https://www.jalview.org/development/jalview_develop/
  - note: null
    type:
    - Repository
    url: https://gitlab.jalview.org/jalview/jalview.git
  - note: Twitter feed
    type:
    - Social media
    url: https://twitter.com/Jalview
  - note: YouTube training videos
    type:
    - Social media
    url: https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw
  - note: null
    type:
    - Social media
    url: https://www.linkedin.com/company/104771886/
  maturity: Mature
  name: Jalview
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: ben_s
  publication:
  - doi: 10.1093/bioinformatics/btp033
    metadata:
      abstract: ''
      authors: []
      citationCount: 7717
      date: '2009-05-07T00:00:00Z'
      journal: Bioinformatics
      title: Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    note: null
    pmcid: PMC2672624
    pmid: '19151095'
    type: []
    version: null
  relation:
  - biotoolsID: jabaws
    type: uses
  - biotoolsID: chimera
    type: uses
  - biotoolsID: chimerax
    type: uses
  - biotoolsID: pymol
    type: uses
  - biotoolsID: bioconda
    type: includedIn
  - biotoolsID: 3d-beacons
    type: uses
  - biotoolsID: uniprot
    type: uses
  - biotoolsID: pfam
    type: uses
  - biotoolsID: ensembl
    type: uses
  - biotoolsID: pdb
    type: uses
  - biotoolsID: rfam
    type: uses
  - biotoolsID: 3d-beacons
    type: uses
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  validated: 1
  version:
  - 2.11.5.1
- accessibility: Open access
  additionDate: '2025-12-10T13:18:28.703003Z'
  biotoolsCURIE: biotools:emapper2gbk
  biotoolsID: emapper2gbk
  collectionID:
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  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Arnaud
    note: null
    orcidid: https://orcid.org/0000-0003-1170-0785
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: https://github.com/ArnaudBelcour
  description: creation of genbank files from Eggnog-mapper annotation outputs
  documentation:
  - note: null
    type:
    - Installation instructions
    - User manual
    url: https://github.com/AuReMe/emapper2gbk
  download:
  - note: null
    type: Source code
    url: https://github.com/AuReMe/emapper2gbk.git
    version: 0.3.2
  - note: null
    type: Software package
    url: https://pypi.org/project/emapper2gbk/#files
    version: 0.3.2
  editPermission:
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    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: genomes -fn genome.fna -fp proteome.faa -gff genome.gff -n "Escherichia coli"
    input:
    - data:
        term: Sequence assembly
        uri: http://edamontology.org/data_0925
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence set (protein)
        uri: http://edamontology.org/data_1233
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
    note: Genomic -single mode
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GenBank-like format (text)
        uri: http://edamontology.org/format_2205
  homepage: https://github.com/AuReMe/emapper2gbk
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-12-10T16:49:05.332576Z'
  license: LGPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/AuReMe/emapper2gbk
  - note: Access to Python library
    type:
    - Software catalogue
    url: https://pypi.org/project/emapper2gbk/
  maturity: Mature
  name: emapper2gbk
  operatingSystem:
  - Linux
  otherID: []
  owner: Noe_Robert
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Data rescue
    uri: http://edamontology.org/topic_4011
  validated: 0
  version:
  - 0.3.2
- accessibility: null
  additionDate: '2020-02-26T09:24:43Z'
  biotoolsCURIE: biotools:South_Green_Genome_Hubs
  biotoolsID: South_Green_Genome_Hubs
  collectionID:
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  confidence_flag: null
  cost: Free of charge
  credit:
  - email: droc@cirad.fr
    fundrefid: null
    gridid: null
    name: Gaetan Droc
    note: null
    orcidid: https://orcid.org/0000-0003-1849-1269
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
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  description: The South Green Genome Hub is a suite of crop-specific community portals
    to manage genomic datasets with focus on tropical and Mediterranean plants. Currently
    developed on Banana, Cacao, Coffee, Grass, Rice, Vanilla, Citrus and Sugarcane,
    genome hubs provide access to multiple datasets (e.g. assemblies, gene product
    information, metabolic pathways, gene families, transcriptomics and genetic markers).
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        uri: http://edamontology.org/data_0968
      format:
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    note: null
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    - term: Genome visualisation
      uri: http://edamontology.org/operation_3208
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    - term: Sequence analysis
      uri: http://edamontology.org/operation_2403
    output:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format: []
  homepage: https://banana-genome-hub.southgreen.fr/
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  language:
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  - PHP
  lastUpdate: '2025-11-27T09:14:28.500250Z'
  license: GPL-2.0
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    type:
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  name: South Green Genome Hubs
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  publication:
  - doi: 10.1093/database/bat035
    metadata:
      abstract: ''
      authors: []
      citationCount: 150
      date: '2013-12-01T00:00:00Z'
      journal: Database
      title: The banana genome hub
    note: null
    pmcid: PMC3662865
    pmid: '23707967'
    type:
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  - doi: 10.1093/nar/gku1108
    metadata:
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      citationCount: 52
      date: '2015-01-28T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The coffee genome hub: A resource for coffee genomes'
    note: null
    pmcid: PMC4383925
    pmid: '25392413'
    type:
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  - doi: 10.1093/hr/uhac221
    metadata:
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      citationCount: 29
      date: '2022-01-01T00:00:00Z'
      journal: Horticulture Research
      title: 'The banana genome hub: a community database for genomics in the Musaceae'
    note: null
    pmcid: PMC9720444
    pmid: '36479579'
    type:
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  - doi: 10.1016/j.xplc.2022.100330
    metadata:
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      citationCount: 26
      date: '2022-09-12T00:00:00Z'
      journal: Plant Communications
      title: A chromosome-level, haplotype-phased Vanilla planifolia genome highlights
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    note: null
    pmcid: PMC9482989
    pmid: '35617961'
    type:
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    version: null
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    type: uses
  - biotoolsID: banana_genome_hub
    type: includes
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  - biotoolsID: cocoa_genome_hub
    type: includes
  - biotoolsID: rice_genome_hub
    type: includes
  - biotoolsID: sugarcane_genome_hub
    type: includes
  - biotoolsID: southgreen
    type: includedIn
  toolType:
  - Database portal
  topic:
  - term: Agricultural science
    uri: http://edamontology.org/topic_3810
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  validated: 0
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- accessibility: Open access
  additionDate: '2019-07-03T16:03:27Z'
  biotoolsCURIE: biotools:MMseqs2
  biotoolsID: MMseqs2
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: 'MMseqs2 (Many-against-Many sequence searching) is a software suite
    to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open
    source software implemented in C++ for Linux, MacOS, and (as beta version, via
    cygwin) Windows. The software is designed to run on multiple cores and servers
    and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST.
    At 100 times its speed it achieves almost the same sensitivity. It can perform
    profile searches with the same sensitivity as PSI-BLAST at over 400 times its
    speed.


    MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales
    linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments
    in 10 h on a single server to 50% sequence identity.'
  documentation:
  - note: null
    type:
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  - note: null
    type:
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  - note: Tutorial material
    type:
    - Training material
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  download:
  - note: null
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    url: https://github.com/soedinglab/MMseqs2/releases
    version: null
  editPermission:
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  function:
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    input:
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        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
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        uri: http://edamontology.org/format_2182
      - term: FASTA-like (text)
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    note: null
    operation:
    - term: Sequence similarity search
      uri: http://edamontology.org/operation_0346
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: BLAST results
        uri: http://edamontology.org/format_1333
  - cmd: 'mmseqs easy-cluster input.fasta output tmp

      mmseqs easy-linclust input.fasta output tmp'
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    note: null
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output:
    - data:
        term: Sequence cluster
        uri: http://edamontology.org/data_1235
      format: []
  - cmd: mmseqs easy-taxonomy query.fasta targetDB output tmp
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTQ-like format (text)
        uri: http://edamontology.org/format_2182
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format: []
  homepage: https://mmseqs.com
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2025-11-10T08:28:33.612233Z'
  license: MIT
  link:
  - note: null
    type:
    - Issue tracker
    url: https://github.com/soedinglab/mmseqs2/issues
  - note: null
    type:
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  maturity: Mature
  name: MMseqs2
  operatingSystem:
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  otherID: []
  owner: milot-mirdita
  publication:
  - doi: 10.1038/nbt.3988
    metadata:
      abstract: ''
      authors: []
      citationCount: 2439
      date: '2017-11-01T00:00:00Z'
      journal: Nature Biotechnology
      title: MMseqs2 enables sensitive protein sequence searching for the analysis
        of massive data sets
    note: null
    pmcid: null
    pmid: '29035372'
    type: []
    version: null
  - doi: 10.1101/079681
    metadata: null
    note: null
    pmcid: null
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    version: null
  - doi: 10.1038/s41467-018-04964-5
    metadata:
      abstract: ''
      authors: []
      citationCount: 577
      date: '2018-12-01T00:00:00Z'
      journal: Nature Communications
      title: Clustering huge protein sequence sets in linear time
    note: null
    pmcid: PMC6026198
    pmid: '29959318'
    type:
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    version: null
  - doi: 10.1093/bioinformatics/bty1057
    metadata:
      abstract: ''
      authors: []
      citationCount: 366
      date: '2019-08-15T00:00:00Z'
      journal: Bioinformatics
      title: MMseqs2 desktop and local web server app for fast, interactive sequence
        searches
    note: null
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    type:
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    version: null
  - doi: 10.1101/2020.11.27.401018
    metadata: null
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    type: []
    version: null
  - doi: 10.1093/bioinformatics/btab184
    metadata:
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      authors: []
      citationCount: 162
      date: '2021-09-15T00:00:00Z'
      journal: Bioinformatics
      title: Fast and sensitive taxonomic assignment to metagenomic contigs
    note: MMseqs2 Taxonomy
    pmcid: PMC8479651
    pmid: '33734313'
    type: []
    version: null
  - doi: 10.1101/2024.11.13.623350v1
    metadata: null
    note: MMseqs2-GPU preprint
    pmcid: null
    pmid: null
    type: []
    version: null
  - doi: 10.1038/s41592-025-02819-8
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-10-01T00:00:00Z'
      journal: Nature Methods
      title: GPU-accelerated homology search with MMseqs2
    note: MMseqs2-GPU
    pmcid: null
    pmid: null
    type: []
    version: null
  relation:
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    type: isNewVersionOf
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    type: includes
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    type: usedBy
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    type: usedBy
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3174
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Proteins
    uri: http://edamontology.org/topic_0078
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  - term: Taxonomy
    uri: http://edamontology.org/topic_0637
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2025-02-28T15:04:33.594183Z'
  biotoolsCURIE: biotools:prolfquapp
  biotoolsID: prolfquapp
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A command-line tool for differential expression analysis in quantitative
    proteomics
  documentation:
  - note: null
    type:
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  download:
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  function:
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      # and again you run the version within the docker container with

      # ./prolfquapp_docker.sh prolfqua_dea.sh -i data_dir/ -d annotation.xlsx -y
      config.yaml -w NameOfAnalysis -s DIANN'
    input:
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    - data:
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      format:
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        uri: http://edamontology.org/format_1929
    note: null
    operation:
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    output:
    - data:
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        uri: http://edamontology.org/data_2603
      format:
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      - term: HTML
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  - cmd: null
    input:
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        uri: http://edamontology.org/data_2603
      format:
      - term: xlsx
        uri: http://edamontology.org/format_3620
    note: null
    operation:
    - term: Validation
      uri: http://edamontology.org/operation_2428
    output:
    - data:
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      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: TSV
        uri: http://edamontology.org/format_3475
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: https://github.com/prolfqua/prolfquapp
  homepage_status: 0
  language:
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  lastUpdate: '2025-11-06T14:37:12.116175Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
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  - note: null
    type:
    - Issue tracker
    url: https://github.com/prolfqua/prolfquapp/issues
  maturity: Emerging
  name: prolfquapp
  operatingSystem:
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  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1021/acs.jproteome.4c00911
    metadata:
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      authors: []
      citationCount: 1
      date: '2025-02-07T00:00:00Z'
      journal: Journal of Proteome Research
      title: prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential
        Expression Analysis in Quantitative Proteomics
    note: null
    pmcid: null
    pmid: null
    type:
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    version: 0.0.6
  relation: []
  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0121
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2016-10-20T10:31:19Z'
  biotoolsCURIE: biotools:peptideshaker
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  collectionID:
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  confidence_flag: null
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  credit:
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    gridid: null
    name: BioInfra.Prot
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: dominik.kopczynski@isas.de
    fundrefid: null
    gridid: null
    name: Dominik Kopczynsk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: http://compomics.github.io/projects/peptide-shaker.html
  description: PeptideShaker is a search engine independent platform for interpretation
    of proteomics identification results from multiple search engines, currently supporting
    X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda
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    PTM localization scores and redoing the protein inference, PeptideShaker attempts
    to give you the best possible understanding of your proteomics data
  documentation:
  - note: null
    type:
    - General
    url: http://compomics.github.io/projects/peptide-shaker.html#read-me
  download:
  - note: null
    type: Source code
    url: https://github.com/compomics/peptide-shaker
    version: null
  editPermission:
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    type: group
  elixirCommunity: []
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  elixir_badge: 0
  function:
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    input:
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        term: Protein sequence
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      format:
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    - data:
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      format:
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        uri: http://edamontology.org/format_3247
    - data:
        term: Mass spectrometry data
        uri: http://edamontology.org/data_2536
      format:
      - term: MGF
        uri: http://edamontology.org/format_3651
    note: null
    operation:
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    - term: Peptide identification
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    - term: Validation
      uri: http://edamontology.org/operation_2428
    - term: PTM localisation
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    - term: Enrichment analysis
      uri: http://edamontology.org/operation_3501
    - term: Structure visualisation
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    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    output:
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      format:
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      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
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      format:
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    - data:
        term: Sequence image
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      format:
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    - data:
        term: Protein report
        uri: http://edamontology.org/data_0896
      format:
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        uri: http://edamontology.org/format_3475
  homepage: http://compomics.github.io/projects/peptide-shaker.html
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2025-11-01T15:59:45.423975Z'
  license: Apache-2.0
  link: []
  maturity: null
  name: PeptideShaker
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: BioInfra.Prot
  publication:
  - doi: 10.1038/nbt.3109
    metadata:
      abstract: ''
      authors: []
      citationCount: 449
      date: '2015-01-01T00:00:00Z'
      journal: Nature Biotechnology
      title: 'PeptideShaker enables reanalysis of MS-derived proteomics data sets:
        To the editor'
    note: null
    pmcid: null
    pmid: '25574629'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Desktop application
  - Command-line tool
  topic:
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Proteomics experiment
    uri: http://edamontology.org/topic_3520
  - term: Proteome
    uri: http://edamontology.org/topic_0644
  validated: 1
  version:
  - 3.0.11
- accessibility: null
  additionDate: '2025-10-29T16:12:04.796577Z'
  biotoolsCURIE: biotools:ngp
  biotoolsID: ngp
  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
  description: Simulation of next-generation proteomics (NGP) based on single-molecule
    sequencing.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output:
    - data:
        term: Simulation
        uri: http://edamontology.org/data_3869
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: https://github.com/magnuspalmblad/NGP
  homepage_status: 0
  language: []
  lastUpdate: '2025-10-29T16:12:04.798957Z'
  license: null
  link: []
  maturity: null
  name: NGP
  operatingSystem: []
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.1021/acs.jproteome.1c00136
    metadata:
      abstract: ''
      authors: []
      citationCount: 5
      date: '2021-06-04T00:00:00Z'
      journal: Journal of Proteome Research
      title: Theoretical Considerations for Next-Generation Proteomics
    note: null
    pmcid: PMC8185883
    pmid: '33904308'
    type:
    - Primary
    version: null
  relation: []
  toolType: []
  topic: []
  validated: 0
  version: []
- accessibility: null
  additionDate: '2025-10-27T16:27:24.014603Z'
  biotoolsCURIE: biotools:netstart_2.0
  biotoolsID: netstart_2.0
  collectionID: []
  confidence_flag: null
  cost: null
  credit:
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    fundrefid: null
    gridid: null
    name: Line Sandvad Nielsen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: henni@dtu.dk
    fundrefid: null
    gridid: null
    name: Henrik Nielsen
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: "Prediction of eukaryotic translation initiation sites using a protein\
    \ language model.\n\nNetStart 2.0 is a deep learning-based model that predicts\
    \ canonical translation initiation sites in mRNA transcripts in species across\
    \ the eukaryotic domain, including vertebrates, invertebrates, plants, fungi,\
    \ and protists. \n\nThe model integrates the ESM-2 protein language model for\
    \ assessing transitions from non-coding to coding regions with local start codon\
    \ sequence context and taxonomical information. It has been trained on sequences\
    \ from 60 phylogenetically diverse eukaryotic species.\n\nIf you need help with\
    \ the bioinformatics programs, see the \"Getting Help\" section at the server\
    \ site at the link."
  documentation: []
  download: []
  editPermission:
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    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Protein identification
      uri: http://edamontology.org/operation_3767
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    - term: Protein modelling
      uri: http://edamontology.org/operation_0477
    - term: Translation initiation site prediction
      uri: http://edamontology.org/operation_0439
    output:
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: https://services.healthtech.dtu.dk/services/NetStart-2.0/
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-10-28T17:34:39.042070Z'
  license: null
  link:
  - note: GitHub with code and instructions and to download and run the program locally
    type:
    - Repository
    url: https://github.com/lsandvad/netstart2
  - note: NetStart 2.0 server where sequences can be uploaded directly without having
      to download the program (hosted by DTU Health Tech).
    type:
    - Service
    url: https://services.healthtech.dtu.dk/services/NetStart-2.0/
  maturity: null
  name: NetStart
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: linesandvad
  publication:
  - doi: 10.1186/S12859-025-06220-2
    metadata:
      abstract: ''
      authors: []
      citationCount: 0
      date: '2025-12-01T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'NetStart 2.0: prediction of eukaryotic translation initiation sites
        using a protein language model'
    note: null
    pmcid: PMC12366053
    pmid: '40830753'
    type:
    - Method
    version: '2.0'
  relation: []
  toolType: []
  topic:
  - term: Gene transcripts
    uri: http://edamontology.org/topic_3512
  - term: Protein expression
    uri: http://edamontology.org/topic_0108
  - term: Gene expression
    uri: http://edamontology.org/topic_0203
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  validated: 0
  version:
  - '2.0'
- accessibility: Open access
  additionDate: '2023-07-26T14:40:01.768324Z'
  biotoolsCURIE: biotools:ms_annika
  biotoolsID: ms_annika
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: viktoria.dorfer@fh-hagenberg.at
    fundrefid: null
    gridid: null
    name: Viktoria Dorfer
    note: null
    orcidid: https://orcid.org/0000-0002-5332-5701
    rorid: null
    typeEntity: Person
    typeRole:
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    url: http://bioinformatics.fh-hagenberg.at/
  - email: micha.birklbauer@fh-hagenberg.at
    fundrefid: null
    gridid: null
    name: Micha Birklbauer
    note: null
    orcidid: https://orcid.org/0009-0005-1051-179X
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: http://bioinformatics.fh-hagenberg.at/
  description: MS Annika is a crosslink search engine based on MS Amanda, aimed at
    identifying crosslinks of cleavable and non-cleavable crosslinkers from MS2 and
    MS3 spectra. It can deal with a wide variety of cross-linkers and provides robust
    and transparent FDR control based on a target-decoy approach. MS Annika is available
    free of charge as a plug-in for Proteome Discoverer.
  documentation:
  - note: null
    type:
    - General
    url: https://hgb-bin-proteomics.github.io/MSAnnika/
  - note: null
    type:
    - User manual
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/MS_Annika_3.0_UserManual.pdf
  - note: Detailed tutorial how to use MS Annika
    type:
    - Training material
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/tutorial/MS_Annika_3.0_Tutorial.pdf
  - note: Detailed tutorial how to use MS Annika
    type:
    - Training material
    url: https://www.youtube.com/watch?v=L1lVt35PYv4
  download:
  - note: Latest MS Annika version for Proteome Disoverer 3.2
    type: Software package
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.2/latest.zip
    version: PD3.2:latest
  - note: Latest MS Annika version for Proteome Disoverer 3.1
    type: Software package
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.1/latest.zip
    version: PD3.1:latest
  - note: Latest MS Annika version for Proteome Disoverer 3.0
    type: Software package
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD3.0/latest.zip
    version: PD3.0:latest
  - note: Latest MS Annika version for Proteome Disoverer 2.5
    type: Software package
    url: https://github.com/hgb-bin-proteomics/MSAnnika/raw/master/releases/latest/PD2.5/latest.zip
    version: PD2.5:latest
  editPermission:
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  elixir_badge: 0
  function:
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    input:
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        term: Mass spectrum
        uri: http://edamontology.org/data_0943
      format:
      - term: MGF
        uri: http://edamontology.org/format_3651
      - term: Thermo RAW
        uri: http://edamontology.org/format_3712
    - data:
        term: Protein sequence record
        uri: http://edamontology.org/data_2886
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Peptide identification
      uri: http://edamontology.org/operation_3631
    - term: Peptide database search
      uri: http://edamontology.org/operation_3646
    - term: PTM localisation
      uri: http://edamontology.org/operation_3755
    - term: PTM identification
      uri: http://edamontology.org/operation_3645
    - term: Target-Decoy
      uri: http://edamontology.org/operation_3649
    output:
    - data:
        term: Sequence search results
        uri: http://edamontology.org/data_0857
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: https://github.com/hgb-bin-proteomics/MSAnnika
  homepage_status: 0
  language:
  - C#
  lastUpdate: '2025-10-26T02:38:48.643054Z'
  license: Freeware
  link:
  - note: MS Annika version archive
    type:
    - Repository
    url: https://github.com/hgb-bin-proteomics/MSAnnika
  maturity: Mature
  name: MS Annika
  operatingSystem:
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  otherID: []
  owner: michabirklbauer
  publication:
  - doi: 10.1021/acs.jproteome.0c01000
    metadata:
      abstract: ''
      authors: []
      citationCount: 22
      date: '2021-05-07T00:00:00Z'
      journal: Journal of Proteome Research
      title: 'MS Annika: A New Cross-Linking Search Engine'
    note: MS Annika for cleavable crosslink identification from MS2 spectra
    pmcid: PMC8155564
    pmid: '33852321'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1021/acs.jproteome.3c00325
    metadata:
      abstract: ''
      authors: []
      citationCount: 5
      date: '2023-09-01T00:00:00Z'
      journal: Journal of Proteome Research
      title: MS Annika 2.0 Identifies Cross-Linked Peptides in MS2-MS3-Based Workflows
        at High Sensitivity and Specificity
    note: MS Annika 2.0 for cleavable crosslink identification from MS3 spectra
    pmcid: PMC10476269
    pmid: '37566781'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1038/s42004-024-01386-x
    metadata:
      abstract: ''
      authors: []
      citationCount: 2
      date: '2024-12-01T00:00:00Z'
      journal: Communications Chemistry
      title: Proteome-wide non-cleavable crosslink identification with MS Annika 3.0
        reveals the structure of the C. elegans Box C/D complex
    note: MS Annika 3.0 for non-cleavable crosslink identification
    pmcid: PMC11659399
    pmid: '39702463'
    type:
    - Primary
    version: '3.0'
  relation:
  - biotoolsID: ms_amanda
    type: uses
  toolType:
  - Plug-in
  topic:
  - term: Protein folding, stability and design
    uri: http://edamontology.org/topic_0130
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  - term: Protein interactions
    uri: http://edamontology.org/topic_0128
  - term: Proteomics
    uri: http://edamontology.org/topic_0121
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version:
  - 'Proteome Discoverer 3.2: MS Annika 3.0 v3.0.7'
  - 'Proteome Discoverer 3.1: MS Annika 3.0 v3.0.7'
  - 'Proteome Discoverer 3.0: MS Annika 2.0 v1.1.4fix'
  - 'Proteome Discoverer 2.5: MS Annika 2.0 v1.1.3'
  - 'Proteome Discoverer 2.4: MS Annika v1.0.0'
  - 'Proteome Discoverer 2.3: MS Annika v1.0.0'
- accessibility: Open access
  additionDate: '2024-05-03T08:43:04.841443Z'
  biotoolsCURIE: biotools:epik
  biotoolsID: epik
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: nromashchenko@lirmm.fr
    fundrefid: null
    gridid: null
    name: Nikolai Romashchenko
    note: null
    orcidid: https://orcid.org/0000-0002-2264-5219
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: rivals@lirmm.fr
    fundrefid: null
    gridid: null
    name: Eric Rivals
    note: null
    orcidid: https://orcid.org/0000-0003-3791-3973
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Precise and scalable evolutionary placement with informative k-mers.
  documentation: []
  download: []
  editPermission:
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  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Data index
        uri: http://edamontology.org/data_0955
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
    note: null
    operation:
    - term: Phylogenetic inference
      uri: http://edamontology.org/operation_0323
    output:
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: https://github.com/phylo42/EPIK
  homepage_status: 0
  language:
  - C++
  - Python
  lastUpdate: '2025-10-02T12:41:03.856493Z'
  license: MIT
  link: []
  maturity: Emerging
  name: EPIK
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: nromashchenko
  publication:
  - doi: 10.1093/BIOINFORMATICS/BTAD692
    metadata:
      abstract: ''
      authors: []
      citationCount: 2
      date: '2023-12-01T00:00:00Z'
      journal: Bioinformatics
      title: 'EPIK: Precise and scalable evolutionary placement with informative k-mers'
    note: null
    pmcid: PMC10701097
    pmid: '37975872'
    type: []
    version: 0.2.0
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  validated: 0
  version:
  - 0.2.0
- accessibility: Open access
  additionDate: '2023-09-05T09:39:45.613658Z'
  biotoolsCURIE: biotools:squarna
  biotoolsID: squarna
  collectionID:
  - 3D-BioInfo-Nucleic-Acid
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: efbaulin@gmail.com
    fundrefid: null
    gridid: null
    name: Eugene F Baulin
    note: https://imol.institute/leaders/baulin-group/
    orcidid: https://orcid.org/0000-0003-4694-9783
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Support
    url: https://scholar.google.com/citations?user=sjfDaUwAAAAJ&hl=en
  description: SQUARNA is a tool for RNA secondary structure prediction. It can take
    a single RNA sequence or an alignment of sequences as input. SQUARNA handles pseudoknots
    and can predict alternative structures. SQUARNA allows structural restraints and
    chemical probing data as additional input and is available at https://github.com/febos/SQUARNA.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/febos/SQUARNA/blob/main/README.md
  - note: pip install SQUARNA
    type:
    - Installation instructions
    url: https://pypi.org/project/SQUARNA/
  download:
  - note: null
    type: Downloads page
    url: https://doi.org/10.5281/zenodo.8292325
    version: '2.3'
  - note: pip install SQUARNA
    type: Software package
    url: https://pypi.org/project/SQUARNA/
    version: '2.3'
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  function:
  - cmd: SQUARNA i=inputfile [OPTIONS]
    input:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: Stockholm format
        uri: http://edamontology.org/format_1961
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
    - data:
        term: Structural profile
        uri: http://edamontology.org/data_0889
      format: []
    note: Input can be a single or several RNA sequences or an alignment of RNA sequences
      along with structural restraints and/or chemical probing data on base reactivities
    operation:
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    output:
    - data:
        term: RNA secondary structure
        uri: http://edamontology.org/data_0880
      format:
      - term: FASTA-like
        uri: http://edamontology.org/format_2546
    - data:
        term: Score
        uri: http://edamontology.org/data_1772
      format: []
  homepage: https://github.com/febos/SQUARNA
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2025-09-26T10:35:19.637909Z'
  license: Apache-2.0
  link:
  - note: GitHub repository
    type:
    - Repository
    url: https://github.com/febos/SQUARNA
  - note: PyPi repository page
    type:
    - Software catalogue
    url: https://pypi.org/project/SQUARNA/
  maturity: Emerging
  name: SQUARNA
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: febos
  publication:
  - doi: 10.1101/2023.08.28.555103
    metadata: null
    note: biorxiv preprint
    pmcid: null
    pmid: null
    type: []
    version: null
  relation: []
  toolType:
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  - Script
  - Library
  topic:
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Nucleic acids
    uri: http://edamontology.org/topic_0077
  - term: Structure analysis
    uri: http://edamontology.org/topic_0081
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  - term: Structure prediction
    uri: http://edamontology.org/topic_0082
  - term: RNA
    uri: http://edamontology.org/topic_0099
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Nucleic acid sites, features and motifs
    uri: http://edamontology.org/topic_3511
  validated: 0
  version:
  - '2.3'
- accessibility: Open access
  additionDate: '2016-03-24T16:22:28Z'
  biotoolsCURIE: biotools:repet
  biotoolsID: repet
  collectionID:
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  - elixir-fr-sdp-2019
  - URGI
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: urgi-repet@versailles.inrae.fr
    fundrefid: null
    gridid: null
    name: URGI
    note: 'This tool has a "Numero de depot APP": FR 001 480007 000 R P 2008 000 31
      235'
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    - Contributor
    - Maintainer
    - Provider
    - Support
    - Documentor
    url: http://urgi.versailles.inrae.fr/
  description: "The REPET package integrates bioinformatics pipelines dedicated to\
    \ detect, annotate and analyze transposable elements (TEs) in genomic sequences.\
    \ The main pipelines are (i) TEdenovo, which search for interspersed repeats,\
    \ build consensus sequences and classify them according to TE features, and (ii)\n\
    \ TEannot, which mines a genome with a library of TE sequences, for instance the\
    \ one produced by the TEdenovo pipeline, to provide TE annotations exported into\
    \ GFF3 files."
  documentation:
  - note: see also https://urgi.versailles.inrae.fr/Tools/REPET/README
    type:
    - General
    url: https://urgi.versailles.inrae.fr/Tools/REPET
  - note: null
    type:
    - Installation instructions
    url: https://urgi.versailles.inrae.fr/Tools/REPET/INSTALL
  - note: See also https://urgi.versailles.inra.fr/Tools/REPET/TEannot-tuto
    type:
    - User manual
    url: https://urgi.versailles.inrae.fr/Tools/REPET/TEdenovo-tuto
  - note: null
    type:
    - Training material
    url: https://forgemia.inra.fr/urgi-anagen/wiki-repet/-/wikis/REPET-V3.0-tutorial
  download:
  - note: null
    type: Source code
    url: https://urgi.versailles.inrae.fr/download/repet/REPET_linux-x64-3.0.tar.gz
    version: v3.0
  editPermission:
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  elixirPlatform:
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  elixir_badge: 0
  function:
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    input:
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        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
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        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Repeat sequence detection
      uri: http://edamontology.org/operation_0379
    - term: Repeat sequence analysis
      uri: http://edamontology.org/operation_0237
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
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        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: Sequence feature table format (text)
        uri: http://edamontology.org/format_2206
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GFF3-seq
        uri: http://edamontology.org/format_1939
  homepage: https://urgi.versailles.inrae.fr/Tools/REPET
  homepage_status: 0
  language:
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  - Python
  lastUpdate: '2025-09-09T08:10:41.737859Z'
  license: CECILL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://urgi.versailles.inrae.fr/download/repet/
  maturity: Legacy
  name: REPET
  operatingSystem:
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  - Mac
  otherID: []
  owner: Institut Francais de Bioinform
  publication:
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    metadata:
      abstract: ''
      authors: []
      citationCount: 226
      date: '2014-05-02T00:00:00Z'
      journal: PLoS ONE
      title: 'PASTEC: An automatic transposable element classification tool'
    note: null
    pmcid: PMC4008368
    pmid: '24786468'
    type:
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    version: null
  - doi: 10.1371/journal.pone.0016526
    metadata:
      abstract: ''
      authors: []
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      date: '2011-02-09T00:00:00Z'
      journal: PLoS ONE
      title: Considering transposable element diversification in de novo annotation
        approaches
    note: null
    pmcid: PMC3031573
    pmid: '21304975'
    type:
    - Primary
    version: null
  - doi: 10.1371/journal.pcbi.0010022
    metadata:
      abstract: ''
      authors: []
      citationCount: 279
      date: '2005-01-01T00:00:00Z'
      journal: PLoS Computational Biology
      title: Combined evidence annotation of transposable elements in genome sequences
    note: null
    pmcid: PMC1185648
    pmid: '16110336'
    type:
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    version: null
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    metadata:
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      authors: []
      citationCount: 65
      date: '2003-12-29T00:00:00Z'
      journal: Journal of Molecular Evolution
      title: Detection of New Transposable Element Families in Drosophila melanogaster
        and Anopheles gambiae Genomes
    note: null
    pmcid: null
    pmid: '15008403'
    type:
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      authors: []
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      date: '2017-03-01T00:00:00Z'
      journal: Proceedings of the IEEE
      title: 'De Novo Annotation of Transposable Elements: Tackling the Fat Genome
        Issue'
    note: null
    pmcid: null
    pmid: null
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: DNA
    uri: http://edamontology.org/topic_0654
  - term: Nucleic acid structure analysis
    uri: http://edamontology.org/topic_0097
  validated: 1
  version:
  - v3.0
- accessibility: Open access
  additionDate: '2016-12-19T14:27:26Z'
  biotoolsCURIE: biotools:fqcleaner
  biotoolsID: fqcleaner
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    gridid: null
    name: Galaxy Support Team
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: Mini workflow for preprocessing fastq files, it includes quality trimming,
    duplicate and artefacts filters for FASTQ read files.
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  download: []
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    - data:
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    - data:
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      format:
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    - data:
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      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence trimming
      uri: http://edamontology.org/operation_3192
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: FASTQ-sanger
        uri: http://edamontology.org/format_1932
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: FASTQ-sanger
        uri: http://edamontology.org/format_1932
    - data:
        term: Data
        uri: http://edamontology.org/data_0006
      format:
      - term: FASTQ-sanger
        uri: http://edamontology.org/format_1932
  homepage: https://gensoft.pasteur.fr/docs/fqCleanER/21.10/
  homepage_status: 0
  language: []
  lastUpdate: '2025-08-27T10:47:14.412802Z'
  license: null
  link:
  - note: null
    type:
    - Galaxy service
    url: https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/odoppelt/fqcleaner/fqCleaner/0.4.1.1
  maturity: Mature
  name: fqcleaner
  operatingSystem: []
  otherID: []
  owner: hmenager
  publication:
  - doi: 10.1093/nar/gkw343
    metadata:
      abstract: High-throughput data production technologies, particularly ‘next-generation’
        DNA sequencing, have ushered in widespread and disruptive changes to biomedical
        research. Making sense of the large datasets produced by these technologies
        requires sophisticated statistical and computational methods, as well as substantial
        computational power. This has led to an acute crisis in life sciences, as
        researchers without informatics training attempt to perform computation-dependent
        analyses. Since 2005, the Galaxy project has worked to address this problem
        by providing a framework that makes advanced computational tools usable by
        non experts. Galaxy seeks to make data-intensive research more accessible,
        transparent and reproducible by providing a Web-based environment in which
        users can perform computational analyses and have all of the details automatically
        tracked for later inspection, publication, or reuse. In this report we highlight
        recently added features enabling biomedical analyses on a large scale.
      authors:
      - name: Afgan E.
      - name: Baker D.
      - name: van den Beek M.
      - name: Blankenberg D.
      - name: Bouvier D.
      - name: Cech M.
      - name: Chilton J.
      - name: Clements D.
      - name: Coraor N.
      - name: Eberhard C.
      - name: Gruning B.
      - name: Guerler A.
      - name: Hillman-Jackson J.
      - name: Kuster G.V.
      - name: Rasche E.
      - name: Soranzo N.
      - name: Turaga N.
      - name: Taylor J.
      - name: Nekrutenko A.
      - name: Goecks J.
      citationCount: 1477
      date: '2016-07-08T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The Galaxy platform for accessible, reproducible and collaborative biomedical
        analyses: 2016 update'
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  - doi: 10.7490/f1000research.1114334.1
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - 0.4.1.1
- accessibility: Open access
  additionDate: '2025-07-23T10:27:57.572501Z'
  biotoolsCURIE: biotools:etenlnc
  biotoolsID: etenlnc
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: barah@tezu.ernet.in
    fundrefid: null
    gridid: null
    name: Pankaj Barah
    note: Assistant Professor at Department of Molecular Biology and Biotechnology,
      Tezpur University.
    orcidid: https://orcid.org/0000-0001-7039-7996
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Maintainer
    url: https://www.tezu.ernet.in/dmbbt/profile/34
  - email: prangannathofficial@gmai.com
    fundrefid: null
    gridid: null
    name: Prangan Nath
    note: null
    orcidid: https://orcid.org/0000-0002-9451-7822
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  description: ETENLNC (End-To-End-Novel-NonCoding) is a lncRNA identification and
    analysis framework
  documentation:
  - note: A detailed guide on running ETENLNC using the demo data can be found in
      the ETENLNC manual (supplementary to our publication)
    type:
    - Command-line options
    url: https://github.com/EvolOMICS-TU/ETENLNC
  download:
  - note: Sample/demo data for ETENLNC. A detailed guide on running ETENLNC using
      the demo data can be found in the ETENLNC manual (supplementary to our publication).
    type: Biological data
    url: https://zenodo.org/records/14325721?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6ImVmYTllNWJkLWE4ODUtNGM3OC05YTAxLWM4ZDk5YTljZDZjMCIsImRhdGEiOnt9LCJyYW5kb20iOiI4M2I1YjBlZDQ4MmUyZTIxNDg2YmI0YTFkMWE5MTI1OCJ9.HeB3WrsPduNzMyXjH4x5HfCgmIp4NzYv0P_11XU9lcXC_ZxEaVndP-kD0LDkxwufHVNlroeAhdK33PR51F6jnw
    version: '1.0'
  editPermission:
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    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: bash ETENLNC_docker.sh
    input:
    - data:
        term: Expression data
        uri: http://edamontology.org/data_2603
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Genome map
        uri: http://edamontology.org/data_1288
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
      - term: GTF
        uri: http://edamontology.org/format_2306
      - term: GFF
        uri: http://edamontology.org/format_2305
    note: Run ETENLNC on paired-end raw RNA-Seq (.fastq) data
    operation:
    - term: Read pre-processing
      uri: http://edamontology.org/operation_3219
    - term: Sequencing quality control
      uri: http://edamontology.org/operation_3218
    - term: Transcriptome assembly
      uri: http://edamontology.org/operation_3258
    - term: Nucleic acid feature detection
      uri: http://edamontology.org/operation_0415
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    - term: Differential gene expression profiling
      uri: http://edamontology.org/operation_3223
    - term: Heat map generation
      uri: http://edamontology.org/operation_0531
    - term: RNA secondary structure prediction
      uri: http://edamontology.org/operation_0278
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    - term: Protein-nucleic acid interaction analysis
      uri: http://edamontology.org/operation_0389
    - term: RNA-binding protein prediction
      uri: http://edamontology.org/operation_3901
    - term: Gene regulatory network prediction
      uri: http://edamontology.org/operation_2437
    output:
    - data:
        term: Nucleic acid sequence record
        uri: http://edamontology.org/data_2887
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Protein interaction data
        uri: http://edamontology.org/data_0906
      format: []
  homepage: https://github.com/EvolOMICS-TU/ETENLNC
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-23T10:27:57.574879Z'
  license: GPL-3.0
  link:
  - note: GitHub Repo
    type:
    - Repository
    url: https://github.com/EvolOMICS-TU/ETENLNC
  maturity: Emerging
  name: ETENLNC
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: prangannath
  publication:
  - doi: 10.1016/j.compbiolchem.2024.108140
    metadata:
      abstract: 'Long non-coding RNAs (lncRNAs) play crucial roles in the regulation
        of gene expression and maintenance of genomic integrity through various interactions
        with DNA, RNA, and proteins. The availability of large-scale sequence data
        from various high-throughput platforms has opened possibilities to identify,
        predict, and functionally annotate lncRNAs. As a result, there is a growing
        demand for an integrative computational framework capable of identifying known
        lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory
        interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding),
        a user-friendly, integrative, open-source, scalable, and modular computational
        framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC
        employs six stringent filtration steps to identify novel lncRNAs, performs
        differential expression analysis of mRNA and lncRNA transcripts, and predicts
        regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked
        ETENLNC against six existing tools and optimized it for desktop workstations
        and high-performance computing environments using data from three different
        species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.'
      authors:
      - name: Nath P.
      - name: Bhuyan K.
      - name: Bhattacharyya D.K.
      - name: Barah P.
      citationCount: 2
      date: '2024-10-01T00:00:00Z'
      journal: Computational Biology and Chemistry
      title: 'ETENLNC: An end to end lncRNA identification and analysis framework
        to facilitate construction of known and novel lncRNA regulatory networks'
    note: null
    pmcid: null
    pmid: '38996755'
    type:
    - Primary
    version: '.0'
  relation:
  - biotoolsID: hisat2
    type: uses
  - biotoolsID: salmon
    type: uses
  - biotoolsID: fastqc
    type: uses
  - biotoolsID: fastp
    type: uses
  - biotoolsID: stringtie
    type: uses
  - biotoolsID: gffcompare
    type: uses
  - biotoolsID: cpc2
    type: uses
  - biotoolsID: ncbi_blast_plus
    type: uses
  - biotoolsID: tximport
    type: uses
  - biotoolsID: deseq2
    type: uses
  - biotoolsID: lnctar
    type: uses
  - biotoolsID: capsule-lpi
    type: uses
  - biotoolsID: seekr
    type: uses
  toolType:
  - Command-line tool
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2025-07-14T08:21:28.942611Z'
  biotoolsCURIE: biotools:UniversalMer
  biotoolsID: UniversalMer
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: UniversalMer is a k-mer counting tool for multiple size of k at once.
    It is available for DNA, RNA, and protein sequences. The program counts and summarizes
    the exact frequency of all k-mers from 1-mer to a user-defined maximum length
    (kmax). Analyzing the k-mer spectrum across multiple values of k can be done in
    seconds. This program is designed for bioinformatics researchers and scientists.
  documentation: []
  download:
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    type: Command-line specification
    url: https://sourceforge.net/projects/universal-mer/
    version: '2.0'
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    input:
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      format:
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        uri: http://edamontology.org/format_2546
    note: null
    operation:
    - term: k-mer counting
      uri: http://edamontology.org/operation_3472
    output:
    - data:
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        uri: http://edamontology.org/data_1266
      format: []
    - data:
        term: Base frequencies table
        uri: http://edamontology.org/data_1265
      format: []
    - data:
        term: Text
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      format: []
  homepage: https://ugrammer.github.io
  homepage_status: 0
  language:
  - C++
  - C
  lastUpdate: '2025-07-14T08:21:28.944946Z'
  license: Freeware
  link:
  - note: null
    type:
    - Mirror
    url: https://sourceforge.net/projects/universal-mer/
  maturity: Emerging
  name: UniversalMer
  operatingSystem:
  - Windows
  - Mac
  otherID: []
  owner: Ugrammer
  publication: []
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 2.0.0
- accessibility: Open access
  additionDate: '2016-02-09T13:19:44Z'
  biotoolsCURIE: biotools:mirgen
  biotoolsID: mirgen
  collectionID:
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  - ELIXIR-NO
  - ELIXIR-Norway
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: BastianFromm@gmail.com
    fundrefid: null
    gridid: null
    name: Bastian Fromm
    note: null
    orcidid: https://orcid.org/0000-0003-0352-3037
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Maintainer
    - Support
    url: null
  - email: kevin.j.peterson@dartmouth.edu
    fundrefid: null
    gridid: null
    name: Kevin J. Peterson
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  - email: support@elixir.no
    fundrefid: null
    gridid: null
    name: The Norwegian Bioinformatics Platform (ELIXIR-Norway) Helpdesk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Consortium
    typeRole:
    - Support
    url: https://elixir.no/helpdesk
  - email: null
    fundrefid: 10.13039/501100005366
    gridid: grid.5510.1
    name: University of Oslo
    note: null
    orcidid: null
    rorid: 01xtthb56
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uio.no/english/index.html
  description: MirGeneDB is a database of manually curated microRNA genes that have
    been validated and annotated as initially described in Fromm et al. 2015 , Fromm
    et al. 2020 and Fromm et al 2022. MirGeneDB 3.0 (Clarke and Hoye et al. 2024 )
    includes more than 21,000 microRNA gene entries representing more than 1,700 microRNA
    families from 114 metazoan species. All microRNAs can be browsed, searched and
    downloaded.
  documentation:
  - note: null
    type:
    - General
    url: https://www.mirgenedb.org/information
  download:
  - note: Sequence downloads for 75 species
    type: Biological data
    url: https://www.mirgenedb.org/download
    version: '3.0'
  editPermission:
    authors:
    - eca008
    type: group
  elixirCommunity: []
  elixirNode:
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  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Organism identifier
        uri: http://edamontology.org/data_1869
      format: []
    note: 'Data retrieval: curated miRNA. Organism identifier: a specific miRNA identifier
      or a species  for all miRNAs for that species. Gene transcript report: with
      metadata and visualization. RNA secondary structure: the hairpin loop of the
      miRNA with bases.'
    operation:
    - term: Data retrieval
      uri: http://edamontology.org/operation_2422
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Gene transcript report
        uri: http://edamontology.org/data_3134
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: RNA secondary structure
        uri: http://edamontology.org/data_0880
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format: []
    note: null
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: RNA sequence
        uri: http://edamontology.org/data_3495
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Sequence coordinates
        uri: http://edamontology.org/data_2012
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
      - term: BED
        uri: http://edamontology.org/format_3003
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://mirgenedb.org/
  homepage_status: 0
  language: []
  lastUpdate: '2025-07-05T22:33:30.082420Z'
  license: CC0-1.0
  link:
  - note: null
    type:
    - Helpdesk
    url: https://elixir.no/helpdesk
  maturity: Mature
  name: MirGeneDB
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID:
  - type: doi
    value: doi:10.25504/FAIRsharing.QXSgvF
    version: '2.0'
  owner: UiO
  publication:
  - doi: 10.1093/nar/gkab1101
    metadata:
      abstract: We describe an update of MirGeneDB, the manually curated microRNA
        gene database. Adhering to uniform and consistent criteria for microRNA annotation
        and nomenclature, we substantially expanded MirGeneDB with 30 additional species
        representing previously missing metazoan phyla such as sponges, jellyfish,
        rotifers and flatworms. MirGeneDB 2.1 now consists of 75 species spanning
        over ∼800 million years of animal evolution, and contains a total number of
        16 670 microRNAs from 1549 families. Over 6000 microRNAs were added in this
        update using ∼550 datasets with ∼7.5 billion sequencing reads. By adding new
        phylogenetically important species, especially those relevant for the study
        of whole genome duplication events, and through updating evolutionary nodes
        of origin for many families and genes, we were able to substantially refine
        our nomenclature system. All changes are traceable in the specifically developed
        MirGeneDB version tracker. The performance of read-pages is improved and microRNA
        expression matrices for all tissues and species are now also downloadable.
        Altogether, this update represents a significant step toward a complete sampling
        of all major metazoan phyla, and a widely needed foundation for comparative
        microRNA genomics and transcriptomics studies. MirGeneDB 2.1 is part of RNAcentral
        and Elixir Norway, publicly and freely available at http://www.mirgenedb.org/.
      authors:
      - name: Fromm B.
      - name: Hoye E.
      - name: Domanska D.
      - name: Zhong X.
      - name: Aparicio-Puerta E.
      - name: Ovchinnikov V.
      - name: Umu S.U.
      - name: Chabot P.J.
      - name: Kang W.
      - name: Aslanzadeh M.
      - name: Tarbier M.
      - name: Marmol-Sanchez E.
      - name: Urgese G.
      - name: Johansen M.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Friedlander M.R.
      - name: Peterson K.J.
      citationCount: 95
      date: '2022-01-07T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 2.1: Toward a complete sampling of all major animal phyla'
    note: null
    pmcid: PMC8728216
    pmid: '34850127'
    type:
    - Primary
    version: '2.1'
  - doi: 10.1093/nar/gkz885
    metadata:
      abstract: Small non-coding RNAs have gained substantial attention due to their
        roles in animal development and human disorders. Among them, microRNAs are
        special because individual gene sequences are conserved across the animal
        kingdom. In addition, unique and mechanistically well understood features
        can clearly distinguish bona fide miRNAs from the myriad other small RNAs
        generated by cells. However, making this distinction is not a common practice
        and, thus, not surprisingly, the heterogeneous quality of available miRNA
        complements has become a major concern in microRNA research. We addressed
        this by extensively expanding our curated microRNA gene database-MirGeneDB-to
        45 organisms, encompassing a wide phylogenetic swath of animal evolution.
        By consistently annotating and naming 10,899 microRNA genes in these organisms,
        we show that previous microRNA annotations contained not only many false positives,
        but surprisingly lacked >2000 bona fide microRNAs. Indeed, curated microRNA
        complements of closely related organisms are very similar and can be used
        to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust
        platform for microRNA-based research, providing deeper and more significant
        insights into the biology and evolution of miRNAs as well as biomedical and
        biomarker research. MirGeneDB is publicly and freely available at http://mirgenedb.org/.
      authors:
      - name: Fromm B.
      - name: Domanska D.
      - name: Hoye E.
      - name: Ovchinnikov V.
      - name: Kang W.
      - name: Aparicio-Puerta E.
      - name: Johansen M.
      - name: Flatmark K.
      - name: Mathelier A.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Friedlander M.R.
      - name: Peterson K.J.
      citationCount: 178
      date: '2020-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 2.0: The metazoan microRNA complement'
    note: null
    pmcid: PMC6943042
    pmid: '31598695'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1146/annurev-genet-120213-092023
    metadata:
      abstract: Although microRNAs (miRNAs) are among the most intensively studied
        molecules of the past 20 years, determining what is and what is not a miRNA
        has not been straightforward. Here, we present a uniform system for the annotation
        and nomenclature of miRNA genes. We show that less than a third of the 1,881
        human miRBase entries, and only approximately 16% of the 7,095 metazoan miRBase
        entries, are robustly supported as miRNA genes. Furthermore, we show that
        the human repertoire of miRNAs has been shaped by periods of intense miRNA
        innovation and that mature gene products show a very different tempo and mode
        of sequence evolution than star products. We establish a new open access database-MirGeneDB
        (http://mirgenedb.org)-to catalog this set of miRNAs, which complements the
        efforts of miRBase but differs from it by annotating the mature versus star
        products and by imposing an evolutionary hierarchy upon this curated and consistently
        named repertoire.
      authors:
      - name: Fromm B.
      - name: Billipp T.
      - name: Peck L.E.
      - name: Johansen M.
      - name: Tarver J.E.
      - name: King B.L.
      - name: Newcomb J.M.
      - name: Sempere L.F.
      - name: Flatmark K.
      - name: Hovig E.
      - name: Peterson K.J.
      citationCount: 435
      date: '2015-11-23T00:00:00Z'
      journal: Annual Review of Genetics
      title: A Uniform System for the Annotation of Vertebrate microRNA Genes and
        the Evolution of the Human microRNAome
    note: null
    pmcid: PMC4743252
    pmid: '26473382'
    type:
    - Primary
    version: '1.0'
  - doi: 10.1093/nar/gkae1094
    metadata:
      abstract: We present a major update of MirGeneDB (3.0), the manually curated
        animal microRNA gene database. Beyond moving to a new server and the creation
        of a computational mirror, we have expanded the database with the addition
        of 33 invertebrate species, including representatives of 5 previously unsampled
        phyla, and 6 mammal species. MirGeneDB now contains entries for 21 822 microRNA
        genes (5160 of these from the new species) belonging to 1743 microRNA families.
        The inclusion of these new species allowed us to refine both the evolutionary
        node of appearance of a number of microRNA genes/families, as well as MirGeneDB's
        phylogenetically informed nomenclature system. Updated covariance models of
        all microRNA families, along with all smallRNA read data are now downloadable.
        These enhanced annotations will allow researchers to analyze microRNA properties
        such as secondary structure and features of their biogenesis within a robust
        phylogenetic context and without the database plagued with numerous false
        positives and false negatives. In light of these improvements, MirGeneDB 3.0
        will assume the responsibility for naming conserved novel metazoan microRNAs.
        MirGeneDB is part of RNAcentral and Elixir Norway and is publicly and freely
        available at mirgenedb.org.
      authors:
      - name: Clarke A.W.
      - name: Hoye E.
      - name: Hembrom A.A.
      - name: Paynter V.M.
      - name: Vinther J.
      - name: Wyrozemski L.
      - name: Biryukova I.
      - name: Formaggioni A.
      - name: Ovchinnikov V.
      - name: Herlyn H.
      - name: Pierce A.
      - name: Wu C.
      - name: Aslanzadeh M.
      - name: Cheneby J.
      - name: Martinez P.
      - name: Friedlander M.R.
      - name: Hovig E.
      - name: Hackenberg M.
      - name: Umu S.U.
      - name: Johansen M.
      - name: Peterson K.J.
      - name: Fromm B.
      citationCount: 6
      date: '2025-01-06T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of
        novel conserved microRNA families and updated covariance models'
    note: null
    pmcid: PMC11701709
    pmid: '39673268'
    type:
    - Primary
    version: '3.0'
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  - term: Gene regulation
    uri: http://edamontology.org/topic_0204
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Zoology
    uri: http://edamontology.org/topic_3500
  - term: Human biology
    uri: http://edamontology.org/topic_2815
  validated: 1
  version:
  - '3.0'
- accessibility: null
  additionDate: '2020-01-14T08:51:14Z'
  biotoolsCURIE: biotools:RepeatModeler2
  biotoolsID: RepeatModeler2
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: RepeatModeler is a de novo transposable element (TE) family identification
    and modeling package. At the heart of RepeatModeler are three de-novo repeat finding
    programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary
    computational methods for identifying repeat element boundaries and family relationships
    from sequence data.
  documentation: []
  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: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: de Novo sequencing
      uri: http://edamontology.org/operation_3644
    - term: Genome annotation
      uri: http://edamontology.org/operation_0362
    output: []
  homepage: https://github.com/Dfam-consortium/RepeatModeler
  homepage_status: 0
  language:
  - Perl
  lastUpdate: '2025-07-01T04:28:03.302129Z'
  license: OSL-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/Dfam-consortium/RepeatModeler/blob/master/LICENSE
  maturity: Mature
  name: RepeatModeler2
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1101/856591
    metadata: null
    note: null
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    pmid: null
    type: []
    version: null
  relation:
  - biotoolsID: repeatmodeler
    type: isNewVersionOf
  toolType:
  - Command-line tool
  topic:
  - term: Model organisms
    uri: http://edamontology.org/topic_0621
  - term: Sequence composition, complexity and repeats
    uri: http://edamontology.org/topic_0157
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  - term: Mobile genetic elements
    uri: http://edamontology.org/topic_0798
  validated: 1
  version:
  - 2.0.7
next: ?page=2
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