List all resources, or create a new resource.

GET /api/t/?outputDataType=%22Sequence%20alignment%22
HTTP 200 OK
Allow: GET, POST, HEAD, OPTIONS
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Vary: Accept

{
    "count": 219,
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        {
            "name": "align-cli",
            "description": "align-cli is a tool to assist manual inspection of mass spectra using alignments, isobaric sequences and other information from mass spectrometry.",
            "homepage": "https://github.com/snijderlab/align-cli",
            "biotoolsID": "align-cli",
            "biotoolsCURIE": "biotools:align-cli",
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                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0292",
                            "term": "Sequence alignment"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1381",
                                "term": "Pair sequence alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_2330",
                                    "term": "Textual format"
                                }
                            ]
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0121",
                    "term": "Proteomics"
                }
            ],
            "operatingSystem": [
                "Mac",
                "Linux",
                "Windows"
            ],
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        {
            "name": "Jalview",
            "description": "Jalview is a free program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.",
            "homepage": "https://www.jalview.org/",
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                    "type": "uses"
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                    "type": "uses"
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                    "type": "uses"
                },
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                    "biotoolsID": "pymol",
                    "type": "uses"
                },
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                    "biotoolsID": "bioconda",
                    "type": "includedIn"
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                {
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                    "type": "uses"
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                    "type": "uses"
                },
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                    "type": "uses"
                },
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                    "biotoolsID": "ensembl",
                    "type": "uses"
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                    "biotoolsID": "pdb",
                    "type": "uses"
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                    "type": "uses"
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                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0564",
                            "term": "Sequence visualisation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0324",
                            "term": "Phylogenetic tree analysis"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3081",
                            "term": "Sequence alignment editing"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1939",
                                    "term": "GFF3-seq"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1982",
                                    "term": "ClustalW format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1961",
                                    "term": "Stockholm format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1984",
                                    "term": "FASTA-aln"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1938",
                                    "term": "GFF2-seq"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1948",
                                    "term": "nbrf/pir"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3774",
                                    "term": "BioJSON (Jalview)"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1997",
                                    "term": "PHYLIP format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3313",
                                    "term": "BLC"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3311",
                                    "term": "RNAML"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1947",
                                    "term": "GCG MSF"
                                },
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                                    "uri": "http://edamontology.org/format_3015",
                                    "term": "Pileup"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1477",
                                    "term": "mmCIF"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3016",
                                    "term": "VCF"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1915",
                                    "term": "Format"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0886",
                                "term": "Structure alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1476",
                                    "term": "PDB"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1948",
                                    "term": "nbrf/pir"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3464",
                                    "term": "JSON"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1961",
                                    "term": "Stockholm format"
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                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
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                                {
                                    "uri": "http://edamontology.org/format_1997",
                                    "term": "PHYLIP format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3313",
                                    "term": "BLC"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3774",
                                    "term": "BioJSON (Jalview)"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1947",
                                    "term": "GCG MSF"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3015",
                                    "term": "Pileup"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1982",
                                    "term": "ClustalW format"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2884",
                                "term": "Plot"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3603",
                                    "term": "PNG"
                                },
                                {
                                    "uri": "http://edamontology.org/format_2331",
                                    "term": "HTML"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3466",
                                    "term": "EPS"
                                },
                                {
                                    "uri": "http://edamontology.org/format_3604",
                                    "term": "SVG"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1915",
                                    "term": "Format"
                                }
                            ]
                        }
                    ],
                    "note": "Other Input formats:\nAMSA (.amsa);\nJnetFile (.concise, .jnet);\nPFAM (.pfam);\nSubstitution matrix (.matrix);\nJalview Project File (.jvp);\nJalview Feature File (.features, .jvfeatures);\nJalview Annotations File (.annotations, .jvannotations);\nPredicted Aligned Error (PAE) Matrix File (.json)\n...\nOther Output formats:\nPFAM (.pfam);\nBioJS (.biojs) (interactive HTML/Javascript);\nJalview Project File (.jvp);",
                    "cmd": null
                }
            ],
            "toolType": [
                "Desktop application",
                "Command-line tool"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_0092",
                    "term": "Data visualisation"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [],
            "license": "GPL-3.0",
            "collectionID": [
                "ELIXIR-UK"
            ],
            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [
                "Tools"
            ],
            "elixirNode": [
                "UK"
            ],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://discourse.jalview.org/",
                    "type": [
                        "Discussion forum"
                    ],
                    "note": null
                },
                {
                    "url": "https://issues.jalview.org/",
                    "type": [
                        "Issue tracker"
                    ],
                    "note": null
                },
                {
                    "url": "https://www.jalview.org/development/jalview_develop/",
                    "type": [
                        "Other"
                    ],
                    "note": "Latest development version"
                },
                {
                    "url": "https://source.jalview.org/crucible/browse/jalview",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                },
                {
                    "url": "https://twitter.com/Jalview",
                    "type": [
                        "Social media"
                    ],
                    "note": "Twitter feed"
                },
                {
                    "url": "https://www.youtube.com/channel/UCIjpnvZB770yz7ftbrJ0tfw",
                    "type": [
                        "Social media"
                    ],
                    "note": "YouTube training videos"
                }
            ],
            "download": [
                {
                    "url": "https://www.jalview.org/download",
                    "type": "Downloads page",
                    "note": null,
                    "version": null
                },
                {
                    "url": "https://www.jalview.org/download/source/",
                    "type": "Source code",
                    "note": null,
                    "version": null
                },
                {
                    "url": "https://www.jalview.org/download/?os=all",
                    "type": "Binaries",
                    "note": "Binaries for all platforms",
                    "version": null
                },
                {
                    "url": "https://www.jalview.org/favicon.svg",
                    "type": "Icon",
                    "note": null,
                    "version": null
                },
                {
                    "url": "https://www.jalview.org/download/other/jar/",
                    "type": "Binaries",
                    "note": "Executable JAR file",
                    "version": null
                }
            ],
            "documentation": [
                {
                    "url": "https://www.jalview.org/about/citation",
                    "type": [
                        "Citation instructions"
                    ],
                    "note": null
                },
                {
                    "url": "https://www.jalview.org/training/",
                    "type": [
                        "Training material"
                    ],
                    "note": "Hands-on exercises, Training courses and Training videos"
                },
                {
                    "url": "https://www.jalview.org/help/faq",
                    "type": [
                        "FAQ"
                    ],
                    "note": null
                },
                {
                    "url": "https://www.jalview.org/help/documentation/",
                    "type": [
                        "User manual"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/bioinformatics/btp033",
                    "pmid": null,
                    "pmcid": null,
                    "type": [],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Jalview Version 2-A multiple sequence alignment editor and analysis workbench",
                        "abstract": "Summary: Jalview Version 2 is a system for interactive WYSIWYG editing, analysis and annotation of multiple sequence alignments. Core features include keyboard and mouse-based editing, multiple views and alignment overviews, and linked structure display with Jmol. Jalview 2 is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. © 2009 The Author(s).",
                        "date": "2009-05-07T00:00:00Z",
                        "citationCount": 6580,
                        "authors": [
                            {
                                "name": "Waterhouse A.M."
                            },
                            {
                                "name": "Procter J.B."
                            },
                            {
                                "name": "Martin D.M.A."
                            },
                            {
                                "name": "Clamp M."
                            },
                            {
                                "name": "Barton G.J."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Jim Procter",
                    "email": null,
                    "url": "http://www.lifesci.dundee.ac.uk/people/jim-procter",
                    "orcidid": "https://orcid.org/0000-0002-7865-7382",
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                    "fundrefid": null,
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                    "note": null
                },
                {
                    "name": "Geoff Barton",
                    "email": null,
                    "url": "https://www.lifesci.dundee.ac.uk/people/geoff-barton",
                    "orcidid": "https://orcid.org/0000-0002-9014-5355",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": null,
                    "typeRole": [],
                    "note": null
                }
            ],
            "community": null,
            "owner": "ben_s",
            "additionDate": "2019-02-13T17:01:40Z",
            "lastUpdate": "2024-05-22T17:28:29.904886Z",
            "editPermission": {
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                    "jimprocter"
                ]
            },
            "validated": 1,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        },
        {
            "name": "MView (EBI)",
            "description": "Reformat the results of a sequence database search (BLAST, FASTA) or a multiple alignment adding optional HTML markup to control colouring and web page layout.",
            "homepage": "https://www.ebi.ac.uk/jdispatcher/msa/mview",
            "biotoolsID": "mview_ebi",
            "biotoolsCURIE": "biotools:mview_ebi",
            "version": [
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                    "operation": [
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                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1948",
                                    "term": "nbrf/pir"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1982",
                                    "term": "ClustalW format"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1948",
                                    "term": "nbrf/pir"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1982",
                                    "term": "ClustalW format"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Web application",
                "Web service"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3071",
                    "term": "Data management"
                },
                {
                    "uri": "http://edamontology.org/topic_0092",
                    "term": "Data visualisation"
                }
            ],
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                "Linux",
                "Windows",
                "Mac"
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            "license": null,
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                "Job Dispatcher Tools"
            ],
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            "link": [
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                    "url": "https://www.ebi.ac.uk/about/contact/support/job-dispatcher-services",
                    "type": [
                        "Helpdesk"
                    ],
                    "note": null
                }
            ],
            "download": [
                {
                    "url": "https://desmid.github.io/mview/",
                    "type": "Downloads page",
                    "note": null,
                    "version": null
                }
            ],
            "documentation": [
                {
                    "url": "http://www.ebi.ac.uk/about/terms-of-use",
                    "type": [
                        "Terms of use"
                    ],
                    "note": null
                },
                {
                    "url": "https://www.ebi.ac.uk/jdispatcher/help",
                    "type": [
                        "General"
                    ],
                    "note": null
                },
                {
                    "url": "https://desmid.github.io/mview/",
                    "type": [
                        "General"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/bioinformatics/14.4.380",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "MView: A web-compatible database search or multiple alignment viewer",
                        "abstract": "Summary: MView is a tool for converting the results of a sequence database search into the form of a coloured multiple alignment of hits stacked against the query. Alternatively, an existing multiple alignment can be processed. In either case, the output is simply HTML, so the result is platform independent and does not require a separate application or applet to be loaded. Availability: Free from http://www.sander.ebi.ac.uk/mview/ subject to copyright restrictions. Contact: brown@@@ebi.ac.uk.",
                        "date": "1998-01-01T00:00:00Z",
                        "citationCount": 289,
                        "authors": [
                            {
                                "name": "Brown N.P."
                            },
                            {
                                "name": "Leroy C."
                            },
                            {
                                "name": "Sander C."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                },
                {
                    "doi": "10.1093/nar/gkae241",
                    "pmid": "38597606",
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": null
                },
                {
                    "doi": "10.1093/nar/gkac240",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Search and sequence analysis tools services from EMBL-EBI in 2022",
                        "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.",
                        "date": "2022-07-05T00:00:00Z",
                        "citationCount": 867,
                        "authors": [
                            {
                                "name": "Madeira F."
                            },
                            {
                                "name": "Pearce M."
                            },
                            {
                                "name": "Tivey A.R.N."
                            },
                            {
                                "name": "Basutkar P."
                            },
                            {
                                "name": "Lee J."
                            },
                            {
                                "name": "Edbali O."
                            },
                            {
                                "name": "Madhusoodanan N."
                            },
                            {
                                "name": "Kolesnikov A."
                            },
                            {
                                "name": "Lopez R."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Nigel Brown",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Developer"
                    ],
                    "note": null
                },
                {
                    "name": "EMBL-EBI",
                    "email": null,
                    "url": null,
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Institute",
                    "typeRole": [
                        "Provider"
                    ],
                    "note": null
                },
                {
                    "name": "Job Dispatcher",
                    "email": null,
                    "url": "https://www.ebi.ac.uk/jdispatcher",
                    "orcidid": null,
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Project",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": null
                }
            ],
            "community": null,
            "owner": "jdispatcher",
            "additionDate": "2015-01-29T15:46:49Z",
            "lastUpdate": "2024-05-16T13:12:03.245759Z",
            "editPermission": {
                "type": "group",
                "authors": [
                    "biomadeira",
                    "nandana"
                ]
            },
            "validated": 1,
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                        "title": "Kalign2: High-performance multiple alignment of protein and nucleotide sequences allowing external features",
                        "abstract": "In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts of data. To address this growing issue we have dramatically improved the running time and memory requirement of Kalign, while maintaining its high alignment accuracy. Kalign version 2 also supports nucleotide alignment, and a newly introduced extension allows for external sequence annotation to be included into the alignment procedure. We demonstrate that Kalign2 is exceptionally fast and memory-efficient, permitting accurate alignment of very large numbers of sequences. The accuracy of Kalign2 compares well to the best methods in the case of protein alignments while its accuracy on nucleotide alignments is generally superior. In addition, we demonstrate the potential of using known or predicted sequence annotation to improve the alignment accuracy. Kalign2 is freely available for download from the Kalign web site (http://msa.sbc.su.se/). © 2008 The Author(s).",
                        "date": "2009-07-24T00:00:00Z",
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                        "authors": [
                            {
                                "name": "Lassmann T."
                            },
                            {
                                "name": "Frings O."
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                            {
                                "name": "Sonnhammer E.L.L."
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                    "metadata": {
                        "title": "Search and sequence analysis tools services from EMBL-EBI in 2022",
                        "abstract": "The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.",
                        "date": "2022-07-05T00:00:00Z",
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                        "authors": [
                            {
                                "name": "Madeira F."
                            },
                            {
                                "name": "Pearce M."
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                            {
                                "name": "Tivey A.R.N."
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                            {
                                "name": "Basutkar P."
                            },
                            {
                                "name": "Lee J."
                            },
                            {
                                "name": "Edbali O."
                            },
                            {
                                "name": "Madhusoodanan N."
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                            {
                                "name": "Kolesnikov A."
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                            {
                                "name": "Lopez R."
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