count: 232
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  additionDate: '2026-06-12T12:09:48.272845Z'
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  cost: Free of charge
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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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  - note: null
    type:
    - User manual
    url: https://genomic-medicine-sweden.github.io/nallo/latest/
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      - term: FASTQ-like format
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    note: null
    operation:
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      uri: http://edamontology.org/operation_3227
    - term: Variant effect prediction
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    - term: Genome assembly
      uri: http://edamontology.org/operation_0525
    - term: Variant prioritisation
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  homepage: https://github.com/genomic-medicine-sweden/nallo
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  language:
  - Groovy
  - Java
  lastUpdate: '2026-06-12T14:03:07.797466Z'
  license: MIT
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    type:
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  name: nallo
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  owner: juan_camilo
  publication:
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    metadata: null
    note: null
    pmcid: PMC12988770
    pmid: '41712762'
    type: []
    version: null
  relation: []
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  - term: Sequence assembly
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  - term: Whole genome sequencing
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  - term: Transcription factors and regulatory sites
    uri: http://edamontology.org/topic_0749
  - term: Epigenetics
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  validated: 0
  version:
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- accessibility: null
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    output:
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    - data:
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    note: 2D interaction diagram drawing and editing
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    note: metal complex geometry prediction
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      - term: PNG
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    input:
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    - data:
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    - data:
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    - data:
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    - data:
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      format:
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    - data:
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    - data:
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    note: PDB mining and protein binding site ensemble generation
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    output:
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    - term: Protein modelling
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- accessibility: null
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  description: SIENA is a software pipeline enabling the fully automated construction
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  - note: null
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    - data:
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    note: PDB mining and protein binding site ensemble generation
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    - data:
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    - data:
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    - data:
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      format:
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    - data:
        term: Database search results
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      format:
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  - note: A web API to run SIENA calculations for protein structures stored in the
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    metadata: null
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    metadata: null
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  description: Genome mapping and spliced alignment of cDNA or amino acid sequences
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    note: null
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    note: null
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  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-05-20T08:59:02.214591Z'
  license: GPL-3.0
  link:
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    type:
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    url: https://github.com/sanger-pathogens/snp-sites
  maturity: null
  name: SNP-sites
  operatingSystem:
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  otherID: []
  owner: aniehues
  publication:
  - doi: 10.1099/mgen.0.000056
    metadata: null
    note: null
    pmcid: PMC5320690
    pmid: '28348851'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: DNA polymorphism
    uri: http://edamontology.org/topic_2885
  validated: 0
  version:
  - 2.5.1
- accessibility: Open access
  additionDate: '2026-05-19T23:23:06.270637Z'
  biotoolsCURIE: biotools:sam2interval
  biotoolsID: sam2interval
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A Python script that converts positional information from a SAM dataset
    into interval format with 0-based start and 1-based end. CIGAR string of SAM format
    is used to compute the end coordinate.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Galaxy
  elixirNode: []
  elixirPlatform: []
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  function:
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    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
    note: null
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
  homepage: https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-19T23:35:39.572272Z'
  license: MIT
  link:
  - note: null
    type:
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    url: https://github.com/galaxyproject/tools-devteam/tree/main/tools/sam2interval
  maturity: Emerging
  name: sam2interval
  operatingSystem:
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  - Windows
  - Linux
  otherID: []
  owner: VKasalica
  publication: []
  relation: []
  toolType:
  - Script
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-05-08T10:33:02.567199Z'
  biotoolsCURIE: biotools:repeatafterme
  biotoolsID: repeatafterme
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
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    fundrefid: null
    gridid: null
    name: Robert Hubley
    note: null
    orcidid: null
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    url: null
  description: RepeatAfterMe is a package for the extension of repetitive DNA cores.
    The tool automatically extends a multiple sequence alignment that may represent
    only a fragment of a longer repetitive sequence family.
  documentation: []
  download: []
  editPermission:
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  function:
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    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: 2bit
        uri: http://edamontology.org/format_3009
    - data:
        term: Sequence range
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      format:
      - term: bed6
        uri: http://edamontology.org/format_3585
    note: null
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
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        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
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        uri: http://edamontology.org/format_1929
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  homepage_status: 0
  language:
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  lastUpdate: '2026-05-08T10:33:02.569259Z'
  license: CC0-1.0
  link: []
  maturity: Mature
  name: RepeatAfterMe
  operatingSystem:
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  otherID: []
  owner: Pub2Tools
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
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- accessibility: null
  additionDate: '2026-05-05T06:03:45.867892Z'
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  collectionID: []
  confidence_flag: null
  cost: null
  credit: []
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  download: []
  editPermission:
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  function:
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    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format: []
    note: null
    operation:
    - term: Base-calling
      uri: http://edamontology.org/operation_3185
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
  homepage: https://github.com/hiruna72/slow5-dorado
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-05-05T06:03:45.870767Z'
  license: Other
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  maturity: null
  name: slow5-dorado
  operatingSystem:
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  otherID: []
  owner: veitveit11
  publication: []
  relation: []
  toolType:
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  topic:
  - term: Long-read sequencing
    uri: http://edamontology.org/topic_4056
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
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- accessibility: null
  additionDate: '2026-05-01T10:45:51.114755Z'
  biotoolsCURIE: biotools:bwa-meth
  biotoolsID: bwa-meth
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: bwa-meth is a tool for alignment of Bisulfite sequencing reads.
  documentation: []
  download: []
  editPermission:
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  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Sequence alignment
      uri: http://edamontology.org/operation_0292
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
  homepage: https://github.com/brentp/bwa-meth
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-05-01T10:45:51.117070Z'
  license: MIT
  link: []
  maturity: Mature
  name: bwa-meth
  operatingSystem:
  - Linux
  otherID: []
  owner: n.m.palmblad@lumc.nl
  publication:
  - doi: 10.48550/arXiv.1401.1129
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Preprint
    version: null
  relation: []
  toolType:
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  topic:
  - term: Mapping
    uri: http://edamontology.org/topic_0102
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  validated: 0
  version:
  - 0.2.9
- accessibility: Open access
  additionDate: '2021-05-06T06:18:52Z'
  biotoolsCURIE: biotools:pangenome-blast
  biotoolsID: pangenome-blast
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Bielefeld University
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uni-bielefeld.de/
  - email: null
    fundrefid: null
    gridid: null
    name: Genome Informatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://gi.cebitec.uni-bielefeld.de/
  - email: plast-service@cebitec.uni-bielefeld.de
    fundrefid: null
    gridid: null
    name: Tizian Schulz
    note: null
    orcidid: https://orcid.org/0000-0003-0744-7078
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: PLAST is a heuristical method to search for highest scoring local alignments
    between a DNA sequence query and a graphical pangenome. It takes as input a plain
    DNA sequence and a pangenome which may either be a set of (multiple) FASTA or
    FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs
    statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard
    output format. Alignments are calculated based on a "seed-and-extend approach"
    while traversing the sequence graph. Biologically meaningful alignments are filtered
    by using an alignment statistic explicitly developed for sequence-to-graph alignments
    involving graphical pangenomes.
  documentation:
  - note: null
    type:
    - General
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.md
  download: []
  editPermission:
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  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLine
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: unambiguous pure nucleotide
        uri: http://edamontology.org/format_1211
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
    note: "In order to search for alignments within the pangenome graph, \nA pangenome\
      \ graph used to search for alignments consists of (1) a file in GFA format containing\
      \ all sequences of the graph, (2) a binary file produced by the tool itself\
      \ or the software \"Bifrost\" and (3) a program-specific index data structure\
      \ in binary format."
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BLAST results
        uri: http://edamontology.org/format_1333
  - cmd: PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fasta
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ
      files are not needed.
    operation:
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
  homepage: https://github.com/tischulz1/plast
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-26T11:22:02.485629Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast
  - note: null
    type:
    - Mirror
    url: https://github.com/tischulz1/plast
  maturity: Mature
  name: PLAST
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: tizian
  publication:
  - doi: 10.1093/bioinformatics/btab077
    metadata:
      abstract: 'Motivation: Increasing amounts of individual genomes sequenced per
        species motivate the usage of pangenomic approaches. Pangenomes may be represented
        as graphical structures, e.g. compacted colored de Bruijn graphs, which offer
        a low memory usage and facilitate reference-free sequence comparisons. While
        sequence-to-graph mapping to graphical pangenomes has been studied for some
        time, no local alignment search tool in the vein of BLAST has been proposed
        yet. Results: We present a new heuristic method to find maximum scoring local
        alignments of a DNA query sequence to a pangenome represented as a compacted
        colored de Bruijn graph. Our approach additionally allows a comparison of
        similarity among sequences within the pangenome. We show that local alignment
        scores follow an exponential-tail distribution similar to BLAST scores, and
        we discuss how to estimate its parameters to separate local alignments representing
        sequence homology from spurious findings. An implementation of our method
        is presented, and its performance and usability are shown. Our approach scales
        sublinearly in running time and memory usage with respect to the number of
        genomes under consideration. This is an advantage over classical methods that
        do not make use of sequence similarity within the pangenome.'
      authors:
      - name: Schulz T.
      - name: Wittler R.
      - name: Rahmann S.
      - name: Hach F.
      - name: Stoye J.
      citationCount: 6
      date: '2021-08-15T00:00:00Z'
      journal: Bioinformatics
      title: Detecting high-scoring local alignments in pangenome graphs
    note: null
    pmcid: PMC8388040
    pmid: '33532821'
    type:
    - Primary
    - Method
    - Benchmarking study
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 0.0.1-0.2.0
- accessibility: Open access (with restrictions)
  additionDate: '2021-03-31T15:26:55Z'
  biotoolsCURIE: biotools:biomas_bioinformatic_analysis_of_metagenomic_amplicons
  biotoolsID: biomas_bioinformatic_analysis_of_metagenomic_amplicons
  collectionID: []
  confidence_flag: tool
  cost: Free of charge (with restrictions)
  credit:
  - email: b.fosso@ibiom.cnr.it
    fundrefid: null
    gridid: null
    name: Bruno Fosso
    note: Researcher at CNR-IBIOM
    orcidid: https://orcid.org/0000-0003-2324-086X
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: graziano.pesole@uniba.it
    fundrefid: null
    gridid: null
    name: Graziano Pesole
    note: Full Professor of Molecular Biology at University of Bari
    orcidid: https://orcid.org/0000-0003-3663-0859
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  - email: m.santamaria@ibiom.cnr.it
    fundrefid: null
    gridid: null
    name: Monica Santamaria
    note: Researcher at CNR-IBIOM
    orcidid: https://orcid.org/0000-0003-1488-6052
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  description: BioMaS is a friendly pipeline for Meta-barcoding HTS data analysis
    specifically designed for users without particular computing skills.
  documentation: []
  download: []
  editPermission:
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    type: private
  elixirCommunity:
  - Marine Metagenomics
  elixirNode:
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  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Taxonomy
        uri: http://edamontology.org/data_3028
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
  - 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: Sequence merging
      uri: http://edamontology.org/operation_0232
    output:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
  - 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: Global alignment
      uri: http://edamontology.org/operation_0496
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: SAM
        uri: http://edamontology.org/format_2573
  homepage: http://itsonewb.cloud.ba.infn.it/galaxy/tool_runner?tool_id=biomas2_wrapper
  homepage_status: 0
  language:
  - Bash
  - Python
  lastUpdate: '2026-01-27T17:22:28.785300Z'
  license: Not licensed
  link: []
  maturity: Emerging
  name: BioMaS (Bioinformatic analysis of Metagenomic amplicons)
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: bfosso
  publication:
  - doi: 10.1186/s12859-015-0595-z
    metadata: null
    note: null
    pmcid: PMC4486701
    pmid: '26130132'
    type:
    - Method
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Omics
    uri: http://edamontology.org/topic_3391
  validated: 0
  version:
  - '1.0'
- accessibility: Open access
  additionDate: '2018-07-29T10:31:55Z'
  biotoolsCURIE: biotools:d-genies
  biotoolsID: d-genies
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Floréal Cabanettes
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: christophe.klopp@inrae.fr
    fundrefid: null
    gridid: null
    name: Christophe Klopp
    note: null
    orcidid: https://orcid.org/0000-0001-7126-5477
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Philippe Bordron
    note: null
    orcidid: https://orcid.org/0000-0003-1975-0920
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Vincent Dominguez
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Developer
    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: D-GENIES – for Dot plot large Genomes in an Interactive, Efficient
    and Simple way – is an online tool designed to compare two genomes. It supports
    large genome and you can interact with the dot plot to improve the visualization.
  documentation:
  - note: null
    type:
    - General
    url: https://dgenies.readthedocs.io/en/latest/index.html
  download: []
  editPermission:
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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: []
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format: []
    note: null
    operation:
    - term: Genome alignment
      uri: http://edamontology.org/operation_3182
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format: []
    - data:
        term: Sequence similarity plot
        uri: http://edamontology.org/data_2161
      format: []
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format: []
    note: null
    operation:
    - term: Dot plot plotting
      uri: http://edamontology.org/operation_0490
    output:
    - data:
        term: Sequence similarity plot
        uri: http://edamontology.org/data_2161
      format: []
  homepage: https://dgenies.toulouse.inrae.fr/
  homepage_status: 0
  language:
  - Python
  - Shell
  lastUpdate: '2025-12-18T10:02:18.098079Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/genotoul-bioinfo/dgenies
  maturity: Mature
  name: D-GENIES
  operatingSystem:
  - Mac
  - Linux
  otherID: []
  owner: d.gabrielaitis
  publication:
  - doi: 10.7717/peerj.4958
    metadata:
      abstract: ''
      authors: []
      citationCount: 493
      date: '2018-01-01T00:00:00Z'
      journal: PeerJ
      title: 'D-GENIES: Dot plot large genomes in an interactive, efficient and simple
        way'
    note: null
    pmcid: PMC5991294
    pmid: '29888139'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version: []
- 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:
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    - ben_s
    - jimprocter
    type: group
  elixirCommunity: []
  elixirNode:
  - UK
  elixirPlatform:
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  - 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: '2016-09-30T15:59:05Z'
  biotoolsCURIE: biotools:silva
  biotoolsID: silva
  collectionID:
  - de.NBI
  - de.NBI-biodata
  - DSMZ Digital Diversity
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: hub@dsmz.de
    fundrefid: null
    gridid: grid.420081.f
    name: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
    note: null
    orcidid: null
    rorid: 02tyer376
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.dsmz.de
  - email: contact@arb-silva.de
    fundrefid: null
    gridid: grid.507782.f
    name: SILVA Team
    note: null
    orcidid: null
    rorid: 027z9pz32
    typeEntity: Division
    typeRole:
    - Primary contact
    url: https://www.arb-silva.de/contact/team/
  description: SILVA provides comprehensive, quality checked and regularly updated
    datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal
    RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukaryota).
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://www.arb-silva.de/silva-license-information/
  - note: null
    type:
    - Citation instructions
    url: https://www.arb-silva.de/contact/
  - note: null
    type:
    - General
    url: https://www.arb-silva.de/documentation/
  - note: null
    type:
    - FAQ
    url: https://www.arb-silva.de/documentation/faqs/
  download:
  - note: SILVA dataset archive
    type: Downloads page
    url: https://www.arb-silva.de/download/archive/
    version: null
  editPermission:
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    type: private
  elixirCommunity: []
  elixirNode:
  - Germany
  elixirPlatform:
  - Data
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence accession (nucleic acid)
        uri: http://edamontology.org/data_1097
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Taxon
        uri: http://edamontology.org/data_1868
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Strain name
        uri: http://edamontology.org/data_1046
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Article ID
        uri: http://edamontology.org/data_1088
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    - data:
        term: Organism name
        uri: http://edamontology.org/data_2909
      format:
      - term: plain text format (unformatted)
        uri: http://edamontology.org/format_1964
    note: The search and retrieval functions of the SILVA website can be used to build
      custom subsets of sequences. In addition to simple searches e.g. for accession
      numbers, organism names, taxonomic entities, or publication DOI/PubMed IDs,
      complex queries over several database fields using constraints such as sequence
      length or quality values are possible. The results can be sorted according to
      accession numbers, organism names, sequence length, sequence and alignment quality
      and Pintail values. The search results show accession number, organism name,
      sequence length, sequence quality values, taxonomic classifications, and links
      to view the full sequence record on SILVA and on ENA. Sequences found via search
      and added to download cart can be downloaded as FASTA and ARB files.
    operation:
    - term: Query and retrieval
      uri: http://edamontology.org/operation_0224
    output:
    - data:
        term: Sequence report
        uri: http://edamontology.org/data_2955
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Sequence alignment (nucleic acid)
        uri: http://edamontology.org/data_1383
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: nucleotide
        uri: http://edamontology.org/format_1207
    - data:
        term: PCR primers
        uri: http://edamontology.org/data_1240
      format:
      - term: nucleotide
        uri: http://edamontology.org/format_1207
    note: "The SILVA Probe Match and Evaluation Tool detects and displays all occurrences\
      \ of a given probe or primer sequence in the SILVA datasets. \n\nTestPrime allows\
      \ you to evaluate the performance of primer pairs by running an in silico PCR\
      \ on the SILVA databases. From the results of the PCR, TestPrime computes coverages\
      \ for each taxonomic group in all of the taxonomies offered by SILVA."
    operation:
    - term: Primer and probe design
      uri: http://edamontology.org/operation_2419
    output:
    - data:
        term: Report
        uri: http://edamontology.org/data_2048
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: HTML
        uri: http://edamontology.org/format_2331
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: Binary format
        uri: http://edamontology.org/format_2333
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    note: The Alignment, Classification and Tree Service (ACT) of SILVA allows to
      align and optionally classify sequences using the SILVA Incremental Aligner
      (SINA). From aligned sequences, (optionally) phylogenetic trees can be inferred
      using FastTree or RAxML.
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Global alignment
      uri: http://edamontology.org/operation_0496
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    - term: Phylogenetic inference (maximum likelihood and Bayesian methods)
      uri: http://edamontology.org/operation_0547
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: ARB
        uri: http://edamontology.org/format_3830
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Sequence alignment report
        uri: http://edamontology.org/data_0867
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Taxonomic classification
        uri: http://edamontology.org/data_1872
      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
  homepage: https://www.arb-silva.de
  homepage_status: 0
  language: []
  lastUpdate: '2025-06-30T13:26:42.882897Z'
  license: CC-BY-4.0
  link:
  - note: SILVA Taxonomy Browser
    type:
    - Service
    url: https://www.arb-silva.de/browser/
  - note: SILVA metadata search
    type:
    - Service
    url: https://www.arb-silva.de/search/
  - note: 'ACT: Alignment, Classification and Tree Service'
    type:
    - Service
    url: https://www.arb-silva.de/aligner/
  - note: SILVA Probe Match and Evaluation Tool
    type:
    - Service
    url: https://www.arb-silva.de/search/testprobe/
  - note: SILVA Primer Evaluation Tool
    type:
    - Service
    url: https://www.arb-silva.de/search/testprime/
  - note: Web-based viewer for the SILVA guide trees
    type:
    - Service
    url: https://treeviewer.arb-silva.de/
  maturity: Mature
  name: SILVA rRNA database
  operatingSystem: []
  otherID:
  - type: rrid
    value: RRID:SCR_006423
    version: null
  owner: silva
  publication:
  - doi: 10.1093/nar/gks1219
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        web resource for up to date, quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. The referred database release 111 (July
        2012) contains 3194 778 small subunit and 288717 large subunit rRNA gene sequences.
        Since the initial description of the project, substantial new features have
        been introduced, including advanced quality control procedures, an improved
        rRNA gene aligner, online tools for probe and primer evaluation and optimized
        browsing, searching and downloading on the website. Furthermore, the extensively
        curated SILVA taxonomy and the new non-redundant SILVA datasets provide an
        ideal reference for high-throughput classification of data from next-generation
        sequencing approaches. © The Author(s) 2012.
      authors:
      - name: Quast C.
      - name: Pruesse E.
      - name: Yilmaz P.
      - name: Gerken J.
      - name: Schweer T.
      - name: Yarza P.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 22633
      date: '2013-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'The SILVA ribosomal RNA gene database project: Improved data processing
        and web-based tools'
    note: null
    pmcid: PMC3531112
    pmid: '23193283'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkt1209
    metadata:
      abstract: SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive
        resource for up-to-date quality-controlled databases of aligned ribosomal
        RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains
        and supplementary online services. SILVA provides a manually curated taxonomy
        for all three domains of life, based on representative phylogenetic trees
        for the small- and large-subunit rRNA genes. This article describes the improvements
        the SILVA taxonomy has undergone in the last 3 years. Specifically we are
        focusing on the curation process, the various resources used for curation
        and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies.
        Our comparisons not only revealed a reasonable overlap between the taxa names,
        but also points to significant differences in both names and numbers of taxa
        between the three resources. © 2013 The Author(s). Published by Oxford University
        Press.
      authors:
      - name: Yilmaz P.
      - name: Parfrey L.W.
      - name: Yarza P.
      - name: Gerken J.
      - name: Pruesse E.
      - name: Quast C.
      - name: Schweer T.
      - name: Peplies J.
      - name: Ludwig W.
      - name: Glockner F.O.
      citationCount: 2590
      date: '2014-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: The SILVA and "all-species Living Tree Project (LTP)" taxonomic frameworks
    note: null
    pmcid: PMC3965112
    pmid: '24293649'
    type:
    - Other
    version: null
  - doi: 10.1093/nar/gkm864
    metadata:
      abstract: 'Sequencing ribosomal RNA (rRNA) genes is currently the method of
        choice for phylogenetic reconstruction, nucleic acid based detection and quantification
        of microbial diversity. The ARB software suite with its corresponding rRNA
        datasets has been accepted by researchers worldwide as a standard tool for
        large scale rRNA analysis. However, the rapid increase of publicly available
        rRNA sequence data has recently hampered the maintenance of comprehensive
        and curated rRNA knowledge databases. A new system, SILVA (from Latin silva,
        forest), was implemented to provide a central comprehensive web resource for
        up to date, quality controlled databases of aligned rRNA sequences from the
        Bacteria, Archaea and Eukarya domains. All sequences are checked for anomalies,
        carry a rich set of sequence associated contextual information, have multiple
        taxonomic classifications, and the latest validly described nomenclature.
        Furthermore, two precompiled sequence datasets compatible with ARB are offered
        for download on the SILVA website: (i) the reference (Ref) datasets, comprising
        only high quality, nearly full length sequences suitable for in-depth phylogenetic
        analysis and probe design and (ii) the comprehensive Parc datasets with all
        publicly available rRNA sequences longer than 300 nucleotides suitable for
        biodiversity analyses. The latest publicly available database release 91 (August
        2007) hosts 547 521 sequences split into 461 823 small subunit and 85 689
        large subunit rRNAs. © 2007 The Author(s).'
      authors:
      - name: Pruesse E.
      - name: Quast C.
      - name: Knittel K.
      - name: Fuchs B.M.
      - name: Ludwig W.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 5291
      date: '2007-12-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'SILVA: A comprehensive online resource for quality checked and aligned
        ribosomal RNA sequence data compatible with ARB'
    note: null
    pmcid: PMC2175337
    pmid: '17947321'
    type:
    - Other
    version: null
  - doi: 10.1093/bioinformatics/bts252
    metadata:
      abstract: 'Motivation: In the analysis of homologous sequences, computation
        of multiple sequence alignments (MSAs) has become a bottleneck. This is especially
        troublesome for marker genes like the ribosomal RNA (rRNA) where already millions
        of sequences are publicly available and individual studies can easily produce
        hundreds of thousands of new sequences. Methods have been developed to cope
        with such numbers, but further improvements are needed to meet accuracy requirements.Results:
        In this study, we present the SILVA Incremental Aligner (SINA) used to align
        the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA
        uses a combination of k-mer searching and partial order alignment (POA) to
        maintain very high alignment accuracy while satisfying high throughput performance
        demands. SINA was evaluated in comparison with the commonly used high throughput
        MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could
        be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising
        38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference
        MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy
        than PyNAST and mothur in all performed benchmarks. © The Author(s) 2012.
        Published by Oxford University Press.'
      authors:
      - name: Pruesse E.
      - name: Peplies J.
      - name: Glockner F.O.
      citationCount: 2408
      date: '2012-07-01T00:00:00Z'
      journal: Bioinformatics
      title: 'SINA: Accurate high-throughput multiple sequence alignment of ribosomal
        RNA genes'
    note: null
    pmcid: PMC3389763
    pmid: '22556368'
    type:
    - Other
    version: null
  - doi: 10.1016/j.jbiotec.2017.06.1198
    metadata:
      abstract: SILVA (lat. forest) is a comprehensive web resource, providing services
        around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA)
        sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back
        to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich
        started the integrated software workbench ARB (lat. tree) to support high-quality
        phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes.
        At that time, the ARB project maintained both, the sequence reference datasets
        and the software package for data analysis. In 2005, with the massive increase
        of DNA sequence data, the maintenance of the software system ARB and the corresponding
        rRNA databases SILVA was split between Munich and the Microbial Genomics and
        Bioinformatics Research Group in Bremen. ARB has been continuously developed
        to include new features and improve the usability of the workbench. Thousands
        of users worldwide appreciate the seamless integration of common analysis
        tools under a central graphical user interface, in combination with its versatility.
        The first SILVA release was deployed in February 2007 based on the EMBL-EBI/ENA
        release 89. Since then, full SILVA releases offering the database content
        in various flavours are published at least annually, complemented by intermediate
        web-releases where only the SILVA web dataset is updated. SILVA is the only
        rDNA database project worldwide where special emphasis is given to the consistent
        naming of clades of uncultivated (environmental) sequences, where no validly
        described cultivated representatives are available. Also exclusive for SILVA
        is the maintenance of both comprehensive aligned 16S/18S rDNA and 23S/28S
        rDNA sequence datasets. Furthermore, the SILVA alignments and trees were designed
        to include Eukaryota, another unique feature among rDNA databases. With the
        termination of the European Ribosomal RNA Database Project in 2007, the SILVA
        database has become the authoritative rDNA database project for Europe. The
        application spectrum of ARB and SILVA ranges from biodiversity analysis, medical
        diagnostics, to biotechnology and quality control for academia and industry.
      authors:
      - name: Glockner F.O.
      - name: Yilmaz P.
      - name: Quast C.
      - name: Gerken J.
      - name: Beccati A.
      - name: Ciuprina A.
      - name: Bruns G.
      - name: Yarza P.
      - name: Peplies J.
      - name: Westram R.
      - name: Ludwig W.
      citationCount: 635
      date: '2017-11-10T00:00:00Z'
      journal: Journal of Biotechnology
      title: 25 years of serving the community with ribosomal RNA gene reference databases
        and tools
    note: null
    pmcid: null
    pmid: '28648396'
    type:
    - Review
    version: null
  - doi: 10.1186/s12859-017-1841-3
    metadata:
      abstract: 'Background: Phylogenetic trees are an important tool to study the
        evolutionary relationships among organisms. The huge amount of available taxa
        poses difficulties in their interactive visualization. This hampers the interaction
        with the users to provide feedback for the further improvement of the taxonomic
        framework. Results: The SILVA Tree Viewer is a web application designed for
        visualizing large phylogenetic trees without requiring the download of any
        software tool or data files. The SILVA Tree Viewer is based on Web Geographic
        Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables
        zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer
        enables access to two phylogenetic (guide) trees provided by the SILVA database:
        the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences,
        clustered at 99% sequence identity and the LSU Ref inferred from high-quality,
        full-length large subunit sequences. Conclusions: The Tree Viewer provides
        tree navigation, search and browse tools as well as an interactive feedback
        system to collect any kinds of requests ranging from taxonomy to data curation
        and improving the tool itself.'
      authors:
      - name: Beccati A.
      - name: Gerken J.
      - name: Quast C.
      - name: Yilmaz P.
      - name: Glockner F.O.
      citationCount: 29
      date: '2017-09-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'SILVA tree viewer: Interactive web browsing of the SILVA phylogenetic
        guide trees'
    note: null
    pmcid: null
    pmid: null
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    - Other
    version: null
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  - term: Microbiology
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  - term: Probes and primers
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    url: null
  - email: null
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    typeEntity: Consortium
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  description: The MuG Virtual Research Environment is an analysis platform for 3D/4D
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  - note: null
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    note: null
    operation:
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    input:
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    - data:
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      format:
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        uri: http://edamontology.org/format_2305
    note: null
    operation:
    - term: Nucleic acid structure prediction
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    - term: Modelling and simulation
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    output:
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      format: []
    - data:
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  - cmd: null
    input:
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      format:
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    note: null
    operation:
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      format:
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  - cmd: null
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    note: null
    operation:
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        term: Nucleic acid features
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      format:
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  - cmd: null
    input:
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      format:
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    note: null
    operation:
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      uri: http://edamontology.org/operation_3927
    - term: Nucleic acid folding analysis
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    output:
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        term: Topology data
        uri: http://edamontology.org/data_3872
      format:
      - term: pickle
        uri: http://edamontology.org/format_4002
    - data:
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      format:
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  - cmd: null
    input:
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    note: null
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      format: []
  - cmd: null
    input:
    - data:
        term: Structure
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    note: null
    operation:
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        term: Trajectory data
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      format: []
  - cmd: null
    input:
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        term: Protein interaction raw data
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      format:
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    note: null
    operation:
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        term: Annotation track
        uri: http://edamontology.org/data_3002
      format:
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  - cmd: null
    input:
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    - data:
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    - data:
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    note: null
    operation:
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    - term: Structure visualisation
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    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
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    output: []
  homepage: https://www.multiscalegenomics.eu/
  homepage_status: 0
  language:
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  - Python
  lastUpdate: '2025-05-29T11:46:19.236621Z'
  license: Apache-2.0
  link:
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    type:
    - Service
    url: http://vre.multiscalegenomics.eu
  - note: null
    type:
    - Repository
    url: https://github.com/Multiscale-Genomics/VRE
  maturity: null
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  owner: lcodo
  publication:
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    metadata: null
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    type:
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  relation:
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    type: includes
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    type: includes
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  toolType:
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  - Workbench
  topic:
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  - term: ChIP-seq
    uri: http://edamontology.org/topic_3169
  - term: Nucleic acid structure analysis
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  biotoolsCURIE: biotools:biosurfdb
  biotoolsID: biosurfdb
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    fundrefid: null
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    note: null
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  description: BioSurfDB is a online database for biodegradation and biosurfactants.
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    note: null
    operation:
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      format: []
    - data:
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    note: null
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      format: []
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  maturity: Mature
  name: BioSurfDB
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  owner: ELIXIR-PT
  publication:
  - doi: 10.1093/database/bav033
    metadata:
      abstract: 'Crude oil extraction, transportation and use provoke the contamination
        of countless ecosystems. Therefore, bioremediation through surfactants mobilization
        or biodegradation is an important subject, both economically and environmentally.
        Bioremediation research had a great boost with the recent advances in Metagenomics,
        as it enabled the sequencing of uncultured microorganisms providing new insights
        on surfactant-producing and/or oil-degrading bacteria. Many research studies
        are making available genomic data from unknown organisms obtained from metagenomics
        analysis of oil-contaminated environmental samples. These new datasets are
        presently demanding the development of new tools and data repositories tailored
        for the biological analysis in a context of bioremediation data analysis.
        This work presents BioSurfDB, www.biosurfdb.org, a curated relational information
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        relevant genes; proteins and their metabolic pathways; (iv) bioremediation
        experiments results, with specific pollutants treatment efficiencies by surfactant
        producing organisms; and (v) a biosurfactant-curated list, grouped by producing
        organism, surfactant name, class and reference. The main goal of this repository
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        mechanisms involved in biosurfactant production and/or biodegradation and
        make it available in a curated way and associated with a number of computational
        tools to support studies of genomic and metagenomic data.'
      authors:
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      - name: Araujo W.
      - name: Sales A.I.L.
      - name: De Brito Guerra A.
      - name: Da Silva Araujo S.C.
      - name: De Vasconcelos A.T.R.
      - name: Agnez-Lima L.F.
      - name: Freitas A.T.
      citationCount: 30
      date: '2015-01-01T00:00:00Z'
      journal: Database
      title: 'BioSurfDB: Knowledge and algorithms to support biosurfactants and biodegradation
        studies'
    note: null
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      format: []
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    name: Vadim Gumerov
    note: null
    orcidid: https://orcid.org/0000-0003-1670-7679
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: TREND is a platform that allows researchers to explore protein function
    and evolution identifying protein features, gene neighborhoods and operons, clustering
    neighboring genes, and integrating all these data into phylogenomic context and
    cross-referencing with RefSeq, Pfam, CDD and MiST databases. The platform provides
    ample opportunities for adjusting each step of the analysis.
  documentation:
  - note: null
    type:
    - User manual
    url: http://trend.evobionet.com/help
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein sequence alignment
        uri: http://edamontology.org/data_1384
      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: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: NCBI locus tag
        uri: http://edamontology.org/data_1900
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: RefSeq accession (protein)
        uri: http://edamontology.org/data_2385
      format: []
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    - term: Phylogenetic inference
      uri: http://edamontology.org/operation_0323
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    - term: Sequence classification
      uri: http://edamontology.org/operation_2995
    - term: Protein domain recognition
      uri: http://edamontology.org/operation_0246
    - term: Protein feature detection
      uri: http://edamontology.org/operation_3092
    output:
    - data:
        term: Protein sequence alignment
        uri: http://edamontology.org/data_1384
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Phylogenetic tree
        uri: http://edamontology.org/data_0872
      format:
      - term: newick
        uri: http://edamontology.org/format_1910
    - data:
        term: Protein features
        uri: http://edamontology.org/data_1277
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format:
      - term: SVG
        uri: http://edamontology.org/format_3604
    - data:
        term: Sequence cluster (protein)
        uri: http://edamontology.org/data_1245
      format:
      - term: JSON
        uri: http://edamontology.org/format_3464
  homepage: http://trend.evobionet.com/
  homepage_status: 0
  language: []
  lastUpdate: '2024-12-17T20:42:49.942166Z'
  license: null
  link: []
  maturity: null
  name: TREND Protein Evolution Function
  operatingSystem: []
  otherID: []
  owner: vadim
  publication:
  - doi: 10.1093/nar/gkaa243
    metadata:
      abstract: Key steps in a computational study of protein function involve analysis
        of (i) relationships between homologous proteins, (ii) protein domain architecture
        and (iii) gene neighborhoods the corresponding proteins are encoded in. Each
        of these steps requires a separate computational task and sets of tools. Currently
        in order to relate protein features and gene neighborhoods information to
        phylogeny, researchers need to prepare all the necessary data and combine
        them by hand, which is time-consuming and error-prone. Here, we present a
        new platform, TREND (tree-based exploration of neighborhoods and domains),
        which can perform all the necessary steps in automated fashion and put the
        derived information into phylogenomic context, thus making evolutionary based
        protein function analysis more efficient. A rich set of adjustable components
        allows a user to run the computational steps specific to his task. TREND is
        freely available at http://trend.zhulinlab.org.
      authors:
      - name: Gumerov V.M.
      - name: Zhulin I.B.
      citationCount: 33
      date: '2021-01-01T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'TREND: a platform for exploring protein function in prokaryotes based
        on phylogenetic, domain architecture and gene neighborhood analyses'
    note: null
    pmcid: PMC7319448
    pmid: '32282909'
    type:
    - Primary
    version: null
  - doi: 10.1093/nar/gkac034
    metadata:
      abstract: TheURL address of the web server published in this article has been
        changed fromhttp://trend.zhulinlab.org to http://trend. evobionet.com/.
      authors:
      - name: Gumerov V.M.
      - name: Zhulin I.B.
      citationCount: 6
      date: '2022-02-22T00:00:00Z'
      journal: Nucleic Acids Research
      title: 'Erratum: TREND: A platform for exploring protein function in prokaryotes
        based on phylogenetic, domain architecture and gene neighborhood analyses
        (Nucleic Acids Research DOI: 10.1093/nar/gkaa243)'
    note: 'Can be also accessed at this URL: https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac034/6517937'
    pmcid: PMC8860576
    pmid: '35100406'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Evolutionary biology
    uri: http://edamontology.org/topic_3299
  - term: Phylogeny
    uri: http://edamontology.org/topic_0084
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Protein sites, features and motifs
    uri: http://edamontology.org/topic_3510
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Phylogenomics
    uri: http://edamontology.org/topic_0194
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: null
  additionDate: '2016-06-02T02:47:10Z'
  biotoolsCURIE: biotools:msa
  biotoolsID: msa
  collectionID:
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  - Bioconductor
  - BioJS
  confidence_flag: null
  cost: Free of charge
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  - email: null
    fundrefid: null
    gridid: null
    name: Sebastian Wilzbach
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Ian Sillitoe
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Guy Yachdav
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Benedikt Rauscher
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Tatyana Goldberg
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Technische Universität München
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
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    name: Google Summer of Code (GSoC) 2014
    note: null
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  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://github.com/wilzbach/msa
  - email: bodenhofer@bioinf.jku.at
    fundrefid: null
    gridid: null
    name: Ulrich Bodenhofer
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
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    url: null
  description: Display multiple-sequence alignment. The tool is also available as
    R/BioConductor interface to the multiple sequence alignment algorithms ClustalW,
    ClustalOmega, and Muscle. All three algorithms are integrated in the package,
    therefore, they do not depend on any external software tools and are available
    for all major platforms.
  documentation:
  - note: null
    type:
    - Terms of use
    url: https://github.com/wilzbach/msa/blob/master/LICENSE
  - note: null
    type:
    - General
    url: http://msa.biojs.net
  download:
  - note: null
    type: Source code
    url: https://github.com/wilzbach/msa
    version: null
  - note: null
    type: Binaries
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    version: null
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  function:
  - cmd: null
    input:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    note: 'Visualizes multiple sequence alignment, calculates conservation, shows
      sequence logo, applies multiple color schemes A multiple sequence alignment
      (ClustalW, FASTA, ...) Exports selected sequences and regions from the alignment
      Images are exported in PNG Export sequences in FASTA format Export features
      in GFF

      NOTE: Actually, all these output types of data should instead be under separate
      "constant" operations, while the visualisation should be an unary operation,
      perhaps without an output.'
    operation:
    - term: Sequence visualisation
      uri: http://edamontology.org/operation_0564
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA-aln
        uri: http://edamontology.org/format_1984
    - data:
        term: Sequence alignment image
        uri: http://edamontology.org/data_1711
      format:
      - term: Image format
        uri: http://edamontology.org/format_3547
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    - data:
        term: Feature table
        uri: http://edamontology.org/data_1270
      format:
      - term: GFF
        uri: http://edamontology.org/format_2305
  - cmd: null
    input:
    - data:
        term: Nucleic acid sequence
        uri: http://edamontology.org/data_2977
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    - data:
        term: Protein sequence
        uri: http://edamontology.org/data_2976
      format:
      - term: nbrf/pir
        uri: http://edamontology.org/format_1948
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: GCG
        uri: http://edamontology.org/format_1935
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: EMBL format
        uri: http://edamontology.org/format_1927
      - term: GenBank format
        uri: http://edamontology.org/format_1936
    note: null
    operation:
    - term: Multiple sequence alignment
      uri: http://edamontology.org/operation_0492
    output:
    - data:
        term: Sequence alignment report
        uri: http://edamontology.org/data_0867
      format:
      - term: ClustalW format
        uri: http://edamontology.org/format_1982
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: PHYLIP format
        uri: http://edamontology.org/format_1997
      - term: PDF
        uri: http://edamontology.org/format_3508
  homepage: http://msa.biojs.net
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2024-11-25T16:17:03.898741Z'
  license: Apache-2.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/wilzbach/msa
  - note: null
    type:
    - Software catalogue
    url: http://biojs.io/
  - note: null
    type:
    - Helpdesk
    url: http://github.com/wilzbach/msa
  - note: null
    type:
    - Mirror
    url: http://www.bioinf.jku.at/software/msa/
  maturity: Mature
  name: msa
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: BioJS
  publication:
  - doi: 10.1093/bioinformatics/btw474
    metadata: null
    note: null
    pmcid: PMC5181560
    pmid: '27412096'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btv494
    metadata: null
    note: null
    pmcid: null
    pmid: '26315911'
    type:
    - Other
    version: null
  relation: []
  toolType:
  - Command-line tool
  - Library
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Phylogenetics
    uri: http://edamontology.org/topic_3293
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  validated: 1
  version:
  - 1.0.0
- accessibility: null
  additionDate: '2015-01-21T15:12:23Z'
  biotoolsCURIE: biotools:crispi
  biotoolsID: crispi
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: GenOuest
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    url: null
  - email: support@genouest.org
    fundrefid: null
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    name: GenOuest platform
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.genouest.org
  description: A CRISPR Interactive database.
  documentation:
  - note: null
    type:
    - General
    url: http://genoweb1.irisa.fr/Serveur-GPO/outils/repeatsAnalysis/CRISPR/help/crispri.pdf
  download: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: A CRISPR Interactive database
    operation:
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://crispi.genouest.org/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:06:25.068541Z'
  license: null
  link: []
  maturity: Mature
  name: Crispi
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
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  publication:
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    metadata: null
    note: null
    pmcid: PMC2788928
    pmid: '19846435'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-01-21T15:12:23Z'
  biotoolsCURIE: biotools:plast
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  cost: Free of charge
  credit:
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    note: null
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  - email: lavenier@irisa.fr
    fundrefid: null
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    name: Dominique Lavenier
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
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    url: null
  description: Parallel Local Alignment Search Tool for Database Comparison.
  documentation:
  - note: null
    type:
    - General
    url: https://plast.inria.fr/
  download: []
  editPermission:
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  function:
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    input:
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    - data:
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      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Sequence alignment
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://www.irisa.fr/symbiose/projects/plast/
  homepage_status: 0
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  license: CECILL-2.0
  link: []
  maturity: Mature
  name: Plast
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: GenOuest
  publication:
  - doi: 10.1186/1471-2105-10-329
    metadata: null
    note: null
    pmcid: PMC2770072
    pmid: '19821978'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1.0'
- accessibility: null
  additionDate: '2015-01-21T15:12:20Z'
  biotoolsCURIE: biotools:cyanolyase
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    note: null
    orcidid: null
    rorid: null
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    typeRole:
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  - email: support@genouest.org
    fundrefid: null
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    note: null
    orcidid: null
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    typeEntity: Person
    typeRole:
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    url: http://www.genouest.org
  description: Manually curated sequence and amino acid motif database gathering all
    the different phycobilin lyases and related protein sequences available in public
    databases.
  documentation:
  - note: null
    type:
    - General
    url: http://cyanolyase.genouest.org/help
  download: []
  editPermission:
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  function:
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    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Motif occurence detection in protein sequences
    operation:
    - term: Sequence feature detection
      uri: http://edamontology.org/operation_0253
    output:
    - data:
        term: Sequence signature matches
        uri: http://edamontology.org/data_0858
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Sequence
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      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: Protein sequence alignment against known family members
    operation:
    - term: Sequence database search
      uri: http://edamontology.org/operation_0338
    output:
    - data:
        term: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: BLAST results
        uri: http://edamontology.org/format_1333
  homepage: http://cyanolyase.genouest.org/
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T16:06:21.263559Z'
  license: null
  link: []
  maturity: Mature
  name: CyanoLyase
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: GenOuest
  publication:
  - doi: 10.1093/nar/gks1091
    metadata: null
    note: null
    pmcid: PMC3531064
    pmid: '23175607'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Gene and protein families
    uri: http://edamontology.org/topic_0623
  validated: 1
  version: []
- accessibility: null
  additionDate: '2017-01-13T13:16:31Z'
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    fundrefid: null
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    name: Slider support
    note: null
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    typeEntity: Person
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    url: null
  description: A suite of java classes which provides alignment of Illumina Sequence
    analyser reads. For alignment it uses base probabilities instead of sequences.
    It also enambles SNP prediction.
  documentation: []
  download: []
  editPermission:
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  function:
  - cmd: null
    input:
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    - data:
        term: Data reference
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    note: null
    operation:
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    - term: SNP detection
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    metadata:
      abstract: Acquired genomic structural variants (SVs) are major hallmarks of
        cancer genomes, but they are challenging to reconstruct from short-read sequencing
        data. Here we exploited the long reads of the nanopore platform using our
        customized pipeline, Picky (https://github.com/TheJacksonLaboratory/Picky),
        to reveal SVs of diverse architecture in a breast cancer model. We identified
        the full spectrum of SVs with superior specificity and sensitivity relative
        to short-read analyses, and uncovered repetitive DNA as the major source of
        variation. Examination of genome-wide breakpoints at nucleotide resolution
        uncovered micro-insertions as the common structural features associated with
        SVs. Breakpoint density across the genome is associated with the propensity
        for interchromosomal connectivity and was found to be enriched in promoters
        and transcribed regions of the genome. Furthermore, we observed an over-representation
        of reciprocal translocations from chromosomal double-crossovers through phased
        SVs. We demonstrate that Picky analysis is an effective tool for comprehensive
        detection of SVs in cancer genomes from long-read data.
      authors:
      - name: Gong L.
      - name: Wong C.-H.
      - name: Cheng W.-C.
      - name: Tjong H.
      - name: Menghi F.
      - name: Ngan C.Y.
      - name: Liu E.T.
      - name: Wei C.-L.
      citationCount: 70
      date: '2018-06-01T00:00:00Z'
      journal: Nature Methods
      title: Picky comprehensively detects high-resolution structural variants in
        nanopore long reads
    note: null
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  - term: Oncology
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      - name: Gentleman R.
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      - name: Bravo H.C.
      - name: Davis S.
      - name: Gatto L.
      - name: Girke T.
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      - name: MaCdonald J.
      - name: Obenchain V.
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      - name: Pages H.
      - name: Reyes A.
      - name: Shannon P.
      - name: Smyth G.K.
      - name: Tenenbaum D.
      - name: Waldron L.
      - name: Morgan M.
      citationCount: 2315
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  description: A database designed to help the mycologist community to access to fungal
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    note: Sequence alignment
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      abstract: 'Background: In environmental sequencing studies, fungi can be identified
        based on nucleic acid sequences, using either highly variable sequences as
        species barcodes or conserved sequences containing a high-quality phylogenetic
        signal. For the latter, identification relies on phylogenetic analyses and
        the adoption of the phylogenetic species concept. Such analysis requires that
        the reference sequences are well identified and deposited in public-access
        databases. However, many entries in the public sequence databases are problematic
        in terms of quality and reliability and these data require screening to ensure
        correct phylogenetic interpretation. Methods and Principal Findings: To facilitate
        phylogenetic inferences and phylogenetic assignment, we introduce a fungal
        sequence database. The database PHYMYCO-DB comprises fungal sequences from
        GenBank that have been filtered to satisfy stringent sequence quality criteria.
        For the first release, two widely used molecular taxonomic markers were chosen:
        the nuclear SSU rRNA and EF1-α gene sequences. Following the automatic extraction
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        while preserving relevant sequences useful for phylogenetic studies. As a
        result of curation, ~20% of the automatically filtered sequences have been
        removed from the database. To demonstrate how PHYMYCO-DB can be employed,
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        sea samples. Conclusion: PHYMYCO-DB offers the tools necessary to: (i) extract
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        levels, (ii) extract already performed alignments, to act as ''reference alignments'',
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        The PHYMYCO-DB is accessible through the URL http://phymycodb.genouest.org.
        © 2012 Mahé et al.'
      authors:
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      - name: Duhamel M.
      - name: Le Calvez T.
      - name: Guillot L.
      - name: Sarbu L.
      - name: Bretaudeau A.
      - name: Collin O.
      - name: Dufresne A.
      - name: Kiers E.T.
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      - name: Carvalho-Silva D.
      - name: Cummins C.
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        two data updates for the previous human assembly, GRCh37, through a dedicated
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    - data:
        term: Sequence alignment report
        uri: http://edamontology.org/data_0867
      format:
      - term: HTML
        uri: http://edamontology.org/format_2331
  homepage: http://antgenomes.org
  homepage_status: 0
  language: []
  lastUpdate: '2024-11-25T14:19:07.736913Z'
  license: null
  link: []
  maturity: null
  name: antgenomes.org
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: bmpvieira
  publication:
  - doi: 10.1186/1471-2164-10-5
    metadata:
      abstract: 'Background: Fourmidable is an infrastructure to curate and share
        the emerging genetic, molecular, and functional genomic data and protocols
        for ants. Description: The Fourmidable assembly pipeline groups nucleotide
        sequences into clusters before independently assembling each cluster. Subsequently,
        assembled sequences are annotated via Interproscan and BLAST against general
        and insect-specific databases. Gene-specific information can be retrieved
        using gene identifiers, searching for similar sequences or browsing through
        inferred Gene Ontology annotations. The database will readily scale as ultra-high
        throughput sequence data and sequences from additional species become available.
        Conclusion: Fourmidable currently houses EST data from two ant species and
        microarray gene expression data for one of these. Fourmidable is publicly
        available at http://fourmidable.unil.ch. © 2009 Wurm et al; licensee BioMed
        Central Ltd.'
      authors:
      - name: Wurm Y.
      - name: Uva P.
      - name: Ricci F.
      - name: Wang J.
      - name: Jemielity S.
      - name: Iseli C.
      - name: Falquet L.
      - name: Keller L.
      citationCount: 38
      date: '2009-01-06T00:00:00Z'
      journal: BMC Genomics
      title: 'Fourmidable: A database for ant genomics'
    note: null
    pmcid: PMC2639375
    pmid: '19126223'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Database portal
  topic:
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Transcriptomics
    uri: http://edamontology.org/topic_3308
  validated: 1
  version: []
- accessibility: null
  additionDate: '2015-08-03T09:36:06Z'
  biotoolsCURIE: biotools:clustalo_ws_jabaws
  biotoolsID: clustalo_ws_jabaws
  collectionID:
  - clustal
  - JABAWS
  confidence_flag: null
  cost: null
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: BioCatalogue
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Documentor
    url: https://www.biocatalogue.org
  - email: null
    fundrefid: null
    gridid: null
    name: null
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: http://www.compbio.dundee.ac.uk/jabaws/contacts.html
  description: JABAWS stands for JAva Bioinformatics Analysis Web Services. It is
    a collection of web services for bioinformatics, and currently provides services
    that make it easy to access well-known multiple sequence alignment and protein
    disorder prediction programs from Jalview.
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.compbio.dundee.ac.uk/jabaws/man_about.html
  - note: null
    type:
    - API documentation
    url: http://www.compbio.dundee.ac.uk/jabaws/full_javadoc/compbio/ws/server/ClustalOWS.html
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence
        uri: http://edamontology.org/data_2044
      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: Sequence alignment
        uri: http://edamontology.org/data_0863
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: http://www.compbio.dundee.ac.uk/jabaws
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2024-11-25T14:17:59.498371Z'
  license: null
  link:
  - note: null
    type:
    - Software catalogue
    url: https://www.biocatalogue.org/services/3687
  maturity: null
  name: ClustalO WS (jabaws)
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: BioCatalogue
  publication:
  - doi: 10.1093/bioinformatics/btr304
    metadata:
      abstract: 'Summary: JABAWS is a web services framework that simplifies the deployment
        of web services for bioinformatics. JABAWS:MSA provides services for five
        multiple sequence alignment (MSA) methods (Probcons, T-coffee, Muscle, Mafft
        and ClustalW), and is the system employed by the Jalview multiple sequence
        analysis workbench since version 2.6. A fully functional, easy to set up server
        is provided as a Virtual Appliance (VA), which can be run on most operating
        systems that support a virtualization environment such as VMware or Oracle
        VirtualBox. JABAWS is also distributed as a Web Application aRchive (WAR)
        and can be configured to run on a single computer and/or a cluster managed
        by Grid Engine, LSF or other queuing systems that support DRMAA. JABAWS:MSA
        provides clients full access to each application''s parameters, allows administrators
        to specify named parameter preset combinations and execution limits for each
        application through simple configuration files. The JABAWS command-line client
        allows integration of JABAWS services into conventional scripts. © The Author(s)
        2011. Published by Oxford University Press.'
      authors:
      - name: Troshin P.V.
      - name: Procter J.B.
      - name: Barton G.J.
      citationCount: 96
      date: '2011-07-01T00:00:00Z'
      journal: Bioinformatics
      title: Java bioinformatics analysis web services for multiple sequence alignment-JABAWS:MSA
    note: null
    pmcid: PMC3129525
    pmid: '21593132'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web service
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 1
  version:
  - '1'
next: ?page=2
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