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{
    "count": 6457,
    "next": "?page=2",
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    "list": [
        {
            "name": "SLiM",
            "description": "Evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios.  Includes a graphical modeling environment.",
            "homepage": "https://messerlab.org/slim/",
            "biotoolsID": "SLiM_software",
            "biotoolsCURIE": "biotools:SLiM_software",
            "version": [
                "3.6"
            ],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0550",
                            "term": "DNA substitution modelling"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3946",
                            "term": "Ecological modelling"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": "Run individual-based evolutionary simulations with explicit genetics",
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool",
                "Desktop application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0610",
                    "term": "Ecology"
                },
                {
                    "uri": "http://edamontology.org/topic_0602",
                    "term": "Molecular interactions, pathways and networks"
                },
                {
                    "uri": "http://edamontology.org/topic_0199",
                    "term": "Genetic variation"
                },
                {
                    "uri": "http://edamontology.org/topic_3299",
                    "term": "Evolutionary biology"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Mac"
            ],
            "language": [
                "C++"
            ],
            "license": "GPL-3.0",
            "collectionID": [],
            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://messerlab.org/slim/",
                    "type": [
                        "Software catalogue"
                    ],
                    "note": "SLiM home page in the Messer Lab website"
                },
                {
                    "url": "https://github.com/MesserLab/SLiM",
                    "type": [
                        "Repository"
                    ],
                    "note": "GitHub repository for SLiM"
                },
                {
                    "url": "https://groups.google.com/g/slim-discuss",
                    "type": [
                        "Discussion forum"
                    ],
                    "note": "Discussion forum for SLiM questions"
                },
                {
                    "url": "https://groups.google.com/g/slim-announce",
                    "type": [
                        "Mailing list"
                    ],
                    "note": "Announcements mailing list"
                }
            ],
            "download": [
                {
                    "url": "http://benhaller.com/slim/SLiM.zip",
                    "type": "Source code",
                    "note": "A source archive for the command-line `slim` tool only.  Complete source code is on GitHub, but most platforms have an installer anyway; see the manual, chapter 2, for installation instructions.",
                    "version": null
                },
                {
                    "url": "https://github.com/MesserLab/SLiM/releases/latest",
                    "type": "Downloads page",
                    "note": "The GitHub page for the current release version, to obtain full source code.",
                    "version": null
                }
            ],
            "documentation": [
                {
                    "url": "http://benhaller.com/slim/SLiM_Manual.pdf",
                    "type": [
                        "User manual"
                    ],
                    "note": "The manual for SLiM itself"
                },
                {
                    "url": "http://benhaller.com/slim/Eidos_Manual.pdf",
                    "type": [
                        "User manual"
                    ],
                    "note": "The manual for Eidos, the scripting language used by SLiM"
                },
                {
                    "url": "http://benhaller.com/slim/SLiMEidosRefSheets.zip",
                    "type": [
                        "Quick start guide"
                    ],
                    "note": "Quick reference sheets for SLiM and Eidos"
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/molbev/msy228",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": "B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond the Wright–Fisher Model. Molecular Biology and Evolution 36(3), 632–637.",
                    "metadata": {
                        "title": "SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model",
                        "abstract": "© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.With the desire to model population genetic processes under increasingly realistic scenarios, forward genetic simulations have become a critical part of the toolbox of modern evolutionary biology. The SLiM forward genetic simulation framework is one of the most powerful and widely used tools in this area. However, its foundation in the Wright-Fisher model has been found to pose an obstacle to implementing many types of models; it is difficult to adapt the Wright-Fisher model, with its many assumptions, to modeling ecologically realistic scenarios such as explicit space, overlapping generations, individual variation in reproduction, density-dependent population regulation, individual variation in dispersal or migration, local extinction and recolonization, mating between subpopulations, age structure, fitness-based survival and hard selection, emergent sex ratios, and so forth. In response to this need, we here introduce SLiM 3, which contains two key advancements aimed at abolishing these limitations. First, the new non-Wright-Fisher or \"nonWF\" model type provides a much more flexible foundation that allows the easy implementation of all of the above scenarios and many more. Second, SLiM 3 adds support for continuous space, including spatial interactions and spatial maps of environmental variables. We provide a conceptual overview of these new features, and present several example models to illustrate their use.",
                        "date": "2019-03-01T00:00:00Z",
                        "citationCount": 143,
                        "authors": [
                            {
                                "name": "Haller B.C."
                            },
                            {
                                "name": "Messer P.W."
                            }
                        ],
                        "journal": "Molecular Biology and Evolution"
                    }
                },
                {
                    "doi": "10.1093/molbev/msy237",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Usage"
                    ],
                    "version": null,
                    "note": "B.C. Haller, P.W. Messer. (2019). Evolutionary modeling in SLiM 3 for beginners. Molecular Biology and Evolution 36(5), 1101–1109.",
                    "metadata": {
                        "title": "Evolutionary Modeling in SLiM 3 for Beginners",
                        "abstract": "© 2019 The Author(s).The SLiM forward genetic simulation framework has proved to be a powerful and flexible tool for population genetic modeling. However, as a complex piece of software with many features that allow simulating a diverse assortment of evolutionary models, its initial learning curve can be difficult. Here we provide a step-by-step demonstration of how to build a simple evolutionary model in SLiM 3, to help new users get started. We will begin with a panmictic neutral model, and build up to a model of the evolution of a polygenic quantitative trait under selection for an environmental phenotypic optimum.",
                        "date": "2019-05-01T00:00:00Z",
                        "citationCount": 1,
                        "authors": [
                            {
                                "name": "Haller B.C."
                            },
                            {
                                "name": "Messer P.W."
                            }
                        ],
                        "journal": "Molecular Biology and Evolution"
                    }
                },
                {
                    "doi": "10.1111/1755-0998.12968",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Method"
                    ],
                    "version": null,
                    "note": "B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019). Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes. Molecular Ecology Resources 19(2), 552–566.",
                    "metadata": {
                        "title": "Tree-sequence recording in SLiM opens new horizons for forward-time simulation of whole genomes",
                        "abstract": "© 2018 John Wiley & Sons LtdThere is an increasing demand for evolutionary models to incorporate relatively realistic dynamics, ranging from selection at many genomic sites to complex demography, population structure, and ecological interactions. Such models can generally be implemented as individual-based forward simulations, but the large computational overhead of these models often makes simulation of whole chromosome sequences in large populations infeasible. This situation presents an important obstacle to the field that requires conceptual advances to overcome. The recently developed tree-sequence recording method (Kelleher, Thornton, Ashander, & Ralph, 2018), which stores the genealogical history of all genomes in the simulated population, could provide such an advance. This method has several benefits: (1) it allows neutral mutations to be omitted entirely from forward-time simulations and added later, thereby dramatically improving computational efficiency; (2) it allows neutral burn-in to be constructed extremely efficiently after the fact, using “recapitation”; (3) it allows direct examination and analysis of the genealogical trees along the genome; and (4) it provides a compact representation of a population's genealogy that can be analysed in Python using the msprime package. We have implemented the tree-sequence recording method in SLiM 3 (a free, open-source evolutionary simulation software package) and extended it to allow the recording of non-neutral mutations, greatly broadening the utility of this method. To demonstrate the versatility and performance of this approach, we showcase several practical applications that would have been beyond the reach of previously existing methods, opening up new horizons for the modelling and exploration of evolutionary processes.",
                        "date": "2019-03-01T00:00:00Z",
                        "citationCount": 33,
                        "authors": [
                            {
                                "name": "Haller B.C."
                            },
                            {
                                "name": "Galloway J."
                            },
                            {
                                "name": "Kelleher J."
                            },
                            {
                                "name": "Messer P.W."
                            },
                            {
                                "name": "Ralph P.L."
                            }
                        ],
                        "journal": "Molecular Ecology Resources"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Philipp Messer",
                    "email": "messer@cornell.edu",
                    "url": "https://messerlab.org",
                    "orcidid": "https://orcid.org/0000-0001-8453-9377",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": null
                },
                {
                    "name": "Benjamin C. Haller",
                    "email": "bhaller@benhaller.com",
                    "url": "http://benhaller.com",
                    "orcidid": "https://orcid.org/0000-0003-1874-8327",
                    "gridid": null,
                    "rorid": null,
                    "fundrefid": null,
                    "typeEntity": "Person",
                    "typeRole": [
                        "Primary contact"
                    ],
                    "note": null
                }
            ],
            "community": null,
            "owner": "bchaller",
            "additionDate": "2019-05-27T16:59:15Z",
            "lastUpdate": "2021-10-17T00:12:21.515331Z",
            "editPermission": {
                "type": "private",
                "authors": []
            },
            "validated": 0,
            "homepage_status": 0,
            "elixir_badge": 0,
            "confidence_flag": null
        },
        {
            "name": "HMMER3",
            "description": "This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search.",
            "homepage": "http://hmmer.org/",
            "biotoolsID": "hmmer3",
            "biotoolsCURIE": "biotools:hmmer3",
            "version": [
                "3.1b1"
            ],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "note": "alimask is used to apply a mask line to a multiple sequence alignment, based on provided alignment or model coordinates.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0492",
                            "term": "Multiple sequence alignment"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0850",
                                "term": "Sequence set"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1916",
                                "term": "Alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1961",
                                    "term": "Stockholm format"
                                }
                            ]
                        }
                    ],
                    "note": "Align sequences to a profile HMM The < hmmfile > should contain only a single profile.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0296",
                            "term": "Sequence profile generation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "note": "Construct profile HMM(s) from multiple sequence alignment(s).",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0336",
                            "term": "Format validation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_3434",
                            "term": "Conversion"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1370",
                                    "term": "HMMER format"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3329",
                                    "term": "HMMER3"
                                }
                            ]
                        }
                    ],
                    "note": "The hmmconvert utility converts an input profile file to different HMMER formats.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0230",
                            "term": "Sequence generation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2044",
                                "term": "Sequence"
                            },
                            "format": []
                        }
                    ],
                    "note": "Sample sequences from a profile HMM.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2422",
                            "term": "Data retrieval"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0968",
                                "term": "Keyword"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "note": "Retrieve profile HMM(s) from a file.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1361",
                                "term": "Position frequency matrix"
                            },
                            "format": []
                        }
                    ],
                    "note": "Given an HMM, produce data required to build an HMM logo.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": "Daemon for searching a protein query against a protein database.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_3329",
                                    "term": "HMMER3"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0955",
                                "term": "Data index"
                            },
                            "format": []
                        }
                    ],
                    "note": "Prepare an HMM database for hmmscan.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1927",
                                    "term": "EMBL format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1936",
                                    "term": "GenBank format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1963",
                                    "term": "UniProtKB format"
                                },
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0957",
                                "term": "Database metadata"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2080",
                                "term": "Database search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search protein sequence(s) against a protein profile database. query sequence to search the target database of profiles Needs to have those four auxiliary binary files generated by hmmpress. The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0850",
                                "term": "Sequence set"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2080",
                                "term": "Database search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search profile(s) against a sequence database. Query profile to search the target database of sequences. Sequence database. Ranked lists of the sequences with the most significant matches to the profile.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_3481",
                            "term": "Probabilistic sequence generation"
                        },
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": []
                        }
                    ],
                    "note": "Collect score distributions on random sequences. The output is a table of numbers, one row for each model. Four different parametric fits to the score data are tested: (1) maximum likelihood fits to both location (mu/tau) and slope (lambda) parameters; (2) assuming lambda=log 2, maximum likelihood fit to the location parameter only; (3) same but assuming an edge- corrected lambda, using current procedures in H3 [Eddy, 2008]; and (4) using both parameters determined by H3s current procedures.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2238",
                            "term": "Statistical calculation"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2048",
                                "term": "Report"
                            },
                            "format": []
                        }
                    ],
                    "note": "Display summary statistics for a profile file. Tabular file of summary statistics for each profile.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0338",
                            "term": "Sequence database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1233",
                                "term": "Sequence set (protein)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Iteratively search sequence(s) against a protein database. database sequence The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0335",
                            "term": "Formatting"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_3494",
                                "term": "DNA sequence"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2044",
                                "term": "Sequence"
                            },
                            "format": []
                        }
                    ],
                    "note": "Build a HMMER binary database file from a sequence file. This binary file may be used as a target database for the DNA search tool nhmmer.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0338",
                            "term": "Sequence database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2977",
                                "term": "Nucleic acid sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1234",
                                "term": "Sequence set (nucleic acid)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search DNA/RNA queries against a DNA/RNA sequence database. nucleic sequence database",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2421",
                            "term": "Database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2977",
                                "term": "Nucleic acid sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1364",
                                "term": "Hidden Markov model"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2080",
                                "term": "Database search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search nucleotide sequence(s) against collections of nucleotide profiles. The <hmmdb> needs to be pressed using hmmpress before it can be searched with hmmscan. The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                },
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0338",
                            "term": "Sequence database search"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_2976",
                                "term": "Protein sequence"
                            },
                            "format": []
                        },
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_1233",
                                "term": "Sequence set (protein)"
                            },
                            "format": []
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0857",
                                "term": "Sequence search results"
                            },
                            "format": []
                        }
                    ],
                    "note": "Search protein sequence(s) against a protein sequence database. database of sequences Ranked lists of the sequences with the most significant matches to the query. The output format is designed to be human-readable, but is often so voluminous that reading it is impractical.",
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool",
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                },
                {
                    "uri": "http://edamontology.org/topic_0160",
                    "term": "Sequence sites, features and motifs"
                },
                {
                    "uri": "http://edamontology.org/topic_0623",
                    "term": "Gene and protein families"
                }
            ],
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                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [
                "Perl",
                "C"
            ],
            "license": "Other",
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                "HMMER",
                "Animal and Crop Genomics"
            ],
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            "cost": null,
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            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/EddyRivasLab/hmmer",
                    "type": [
                        "Repository"
                    ],
                    "note": null
                },
                {
                    "url": "https://github.com/EddyRivasLab/hmmer/issues",
                    "type": [
                        "Issue tracker"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [
                {
                    "url": "http://eddylab.org/software/hmmer3/3.1b2/Userguide.pdf",
                    "type": [
                        "User manual"
                    ],
                    "note": "HMMER User Guide"
                },
                {
                    "url": "http://hmmer.org/documentation.html",
                    "type": [
                        "General"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1093/nar/gkr367",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "HMMER web server: Interactive sequence similarity searching",
                        "abstract": "HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use. Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions. It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web. A HMMER web server (http://hmmer.janelia.org) has been designed and implemented such that most protein database searches return within a few seconds. Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam. The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once. All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows. We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them. © 2011 The Author(s).",
                        "date": "2011-07-01T00:00:00Z",
                        "citationCount": 2484,
                        "authors": [
                            {
                                "name": "Finn R.D."
                            },
                            {
                                "name": "Clements J."
                            },
                            {
                                "name": "Eddy S.R."
                            }
                        ],
                        "journal": "Nucleic Acids Research"
                    }
                },
                {
                    "doi": "10.1371/journal.pcbi.1002195",
                    "pmid": "22039361",
                    "pmcid": "PMC3197634",
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Accelerated profile HMM searches",
                        "abstract": "Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been hindered by the computational expense of existing software implementations. Here I describe an acceleration heuristic for profile HMMs, the \"multiple segment Viterbi\" (MSV) algorithm. The MSV algorithm computes an optimal sum of multiple ungapped local alignment segments using a striped vector-parallel approach previously described for fast Smith/Waterman alignment. MSV scores follow the same statistical distribution as gapped optimal local alignment scores, allowing rapid evaluation of significance of an MSV score and thus facilitating its use as a heuristic filter. I also describe a 20-fold acceleration of the standard profile HMM Forward/Backward algorithms using a method I call \"sparse rescaling\". These methods are assembled in a pipeline in which high-scoring MSV hits are passed on for reanalysis with the full HMM Forward/Backward algorithm. This accelerated pipeline is implemented in the freely available HMMER3 software package. Performance benchmarks show that the use of the heuristic MSV filter sacrifices negligible sensitivity compared to unaccelerated profile HMM searches. HMMER3 is substantially more sensitive and 100- to 1000-fold faster than HMMER2. HMMER3 is now about as fast as BLAST for protein searches. © 2011 Sean R. Eddy.",
                        "date": "2011-10-01T00:00:00Z",
                        "citationCount": 2414,
                        "authors": [
                            {
                                "name": "Eddy S.R."
                            }
                        ],
                        "journal": "PLoS Computational Biology"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Sean Eddy",
                    "email": "sean@eddylab.org",
                    "url": null,
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                    ],
                    "note": null
                }
            ],
            "community": {
                "biolib": {
                    "app_name": "hmmsearch",
                    "author_name": "HMMER",
                    "author_username": "HMMER"
                }
            },
            "owner": "ELIXIR-FR",
            "additionDate": "2015-04-03T13:17:38Z",
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            },
            "validated": 1,
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            "confidence_flag": null
        },
        {
            "name": "MAFFT",
            "description": "MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program.",
            "homepage": "http://mafft.cbrc.jp/alignment/server/index.html",
            "biotoolsID": "MAFFT",
            "biotoolsCURIE": "biotools:MAFFT",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0492",
                            "term": "Multiple sequence alignment"
                        }
                    ],
                    "input": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        }
                    ],
                    "output": [
                        {
                            "data": {
                                "uri": "http://edamontology.org/data_0863",
                                "term": "Sequence alignment"
                            },
                            "format": [
                                {
                                    "uri": "http://edamontology.org/format_1929",
                                    "term": "FASTA"
                                }
                            ]
                        }
                    ],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Command-line tool",
                "Web application"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_0080",
                    "term": "Sequence analysis"
                }
            ],
            "operatingSystem": [
                "Linux",
                "Windows",
                "Mac"
            ],
            "language": [
                "Python"
            ],
            "license": "BSD-Source-Code",
            "collectionID": [
                "galaxyPasteur",
                "MAFFT"
            ],
            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": "Open access",
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://galaxy.pasteur.fr/tool_runner?tool_id=toolshed.pasteur.fr/repos/fmareuil/mafft/rbc_mafft/7.273.1",
                    "type": [
                        "Galaxy service"
                    ],
                    "note": null
                }
            ],
            "download": [
                {
                    "url": "https://mafft.cbrc.jp/alignment/software/",
                    "type": "Downloads page",
                    "note": null,
                    "version": null
                }
            ],
            "documentation": [
                {
                    "url": "https://mafft.cbrc.jp/alignment/software/tips0.html",
                    "type": [
                        "FAQ"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1007/978-1-62703-646-7_8",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "MAFFT: Iterative refinement and additional methods",
                        "abstract": "This chapter outlines several methods implemented in the MAFFT package. MAFFT is a popular multiple sequence alignment (MSA) program with various options for the progressive method, the iterative refinement method and other methods. We first outline basic usage of MAFFT and then describe recent practical extensions, such as dot plot and adjustment of direction in DNA alignment. We also refer to MUSCLE, another high-performance MSA program. © 2014 Springer Science+Business Media, LLC.",
                        "date": "2014-01-01T00:00:00Z",
                        "citationCount": 232,
                        "authors": [
                            {
                                "name": "Katoh K."
                            },
                            {
                                "name": "Standley D.M."
                            }
                        ],
                        "journal": "Methods in Molecular Biology"
                    }
                },
                {
                    "doi": "10.7490/f1000research.1114334.1",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": null
                },
                {
                    "doi": "10.1093/bioinformatics/bty121",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Parallelization of MAFFT for large-scale multiple sequence alignments",
                        "abstract": "© The Author(s) 2018. Published by Oxford University Press.Summary: We report an update for the MAFFT multiple sequence alignment program to enable parallel calculation of large numbers of sequences. The G-INS-1 option of MAFFT was recently reported to have higher accuracy than other methods for large data, but this method has been impractical for most large-scale analyses, due to the requirement of large computational resources. We introduce a scalable variant, G-large-INS-1, which has equivalent accuracy to G-INS-1 and is applicable to 50 000 or more sequences.",
                        "date": "2018-07-15T00:00:00Z",
                        "citationCount": 238,
                        "authors": [
                            {
                                "name": "Nakamura T."
                            },
                            {
                                "name": "Yamada K.D."
                            },
                            {
                                "name": "Tomii K."
                            },
                            {
                                "name": "Katoh K."
                            }
                        ],
                        "journal": "Bioinformatics"
                    }
                },
                {
                    "doi": "10.1093/bib/bbx108",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Other"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "MAFFT online service: Multiple sequence alignment, interactive sequence choice and visualization",
                        "abstract": "© 2017 The Author. Published by Oxford University Press.This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.",
                        "date": "2018-03-27T00:00:00Z",
                        "citationCount": 1615,
                        "authors": [
                            {
                                "name": "Katoh K."
                            },
                            {
                                "name": "Rozewicki J."
                            },
                            {
                                "name": "Yamada K.D."
                            }
                        ],
                        "journal": "Briefings in Bioinformatics"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Contact Form",
                    "email": null,
                    "url": "https://mafft.cbrc.jp/alignment/software/mailform.html",
                    "orcidid": null,
                    "gridid": null,
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                    ],
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                }
            ],
            "community": {
                "biolib": {
                    "app_name": "MAFFT",
                    "author_name": "bio-utils",
                    "author_username": "bio-utils"
                }
            },
            "owner": "jison",
            "additionDate": "2017-12-06T18:14:39Z",
            "lastUpdate": "2021-10-15T13:58:17.883534Z",
            "editPermission": {
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                    "laurasansc"
                ]
            },
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            "homepage_status": 0,
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            "confidence_flag": null
        },
        {
            "name": "msprime",
            "description": "Msprime is a Python package that simulates ancestral histories and DNA sequence data. Msprime uses backwards-in-time \"coalescent\" models which allows it to simulate data very efficiently; however, it is not as flexible as forwards-in-time simulators (e.g. SLiM, fwdpy11).",
            "homepage": "https://tskit.dev/msprime",
            "biotoolsID": "msprime",
            "biotoolsCURIE": "biotools:msprime",
            "version": [],
            "otherID": [],
            "relation": [
                {
                    "biotoolsID": "ms",
                    "type": "isNewVersionOf"
                }
            ],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_2426",
                            "term": "Modelling and simulation"
                        }
                    ],
                    "input": [],
                    "output": [],
                    "note": null,
                    "cmd": null
                }
            ],
            "toolType": [
                "Library"
            ],
            "topic": [
                {
                    "uri": "http://edamontology.org/topic_3056",
                    "term": "Population genetics"
                }
            ],
            "operatingSystem": [],
            "language": [
                "Python"
            ],
            "license": "GPL-3.0",
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            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [
                {
                    "url": "https://github.com/tskit-dev/msprime",
                    "type": [
                        "Repository",
                        "Issue tracker"
                    ],
                    "note": null
                },
                {
                    "url": "https://github.com/tskit-dev/msprime/discussions",
                    "type": [
                        "Discussion forum",
                        "Helpdesk"
                    ],
                    "note": null
                }
            ],
            "download": [],
            "documentation": [
                {
                    "url": "https://tskit.dev/msprime/docs/latest",
                    "type": [
                        "General"
                    ],
                    "note": null
                }
            ],
            "publication": [
                {
                    "doi": "10.1371/journal.pcbi.1004842",
                    "pmid": null,
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": null,
                    "note": null,
                    "metadata": {
                        "title": "Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes",
                        "abstract": "© 2016 Kelleher et al.A central challenge in the analysis of genetic variation is to provide realistic genome simulation across millions of samples. Present day coalescent simulations do not scale well, or use approximations that fail to capture important long-range linkage properties. Analysing the results of simulations also presents a substantial challenge, as current methods to store genealogies consume a great deal of space, are slow to parse and do not take advantage of shared structure in correlated trees. We solve these problems by introducing sparse trees and coalescence records as the key units of genealogical analysis. Using these tools, exact simulation of the coalescent with recombination for chromosome-sized regions over hundreds of thousands of samples is possible, and substantially faster than present-day approximate methods. We can also analyse the results orders of magnitude more quickly than with existing methods.",
                        "date": "2016-05-01T00:00:00Z",
                        "citationCount": 161,
                        "authors": [
                            {
                                "name": "Kelleher J."
                            },
                            {
                                "name": "Etheridge A.M."
                            },
                            {
                                "name": "McVean G."
                            }
                        ],
                        "journal": "PLoS Computational Biology"
                    }
                }
            ],
            "credit": [],
            "community": null,
            "owner": "castedo",
            "additionDate": "2021-10-12T12:30:24.762169Z",
            "lastUpdate": "2021-10-12T14:24:17.312443Z",
            "editPermission": {
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                "authors": [
                    "bchaller"
                ]
            },
            "validated": 0,
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            "confidence_flag": null
        },
        {
            "name": "MoFi",
            "description": "MoFi annotates glycoprotein mass spectra by integrating hybrid data from the intact protein and glycopeptide level.",
            "homepage": "https://github.com/cdl-biosimilars/mofi/",
            "biotoolsID": "mofi",
            "biotoolsCURIE": "biotools:mofi",
            "version": [
                "1.1"
            ],
            "otherID": [],
            "relation": [],
            "function": [],
            "toolType": [
                "Desktop application"
            ],
            "topic": [],
            "operatingSystem": [
                "Windows",
                "Linux"
            ],
            "language": [
                "Python"
            ],
            "license": "MIT",
            "collectionID": [],
            "maturity": "Mature",
            "cost": "Free of charge",
            "accessibility": null,
            "elixirPlatform": [],
            "elixirNode": [],
            "elixirCommunity": [],
            "link": [],
            "download": [
                {
                    "url": "https://github.com/cdl-biosimilars/mofi/releases/tag/v1.1",
                    "type": "Source code",
                    "note": null,
                    "version": "1.1"
                }
            ],
            "documentation": [],
            "publication": [
                {
                    "doi": "10.1021/acs.analchem.8b00019",
                    "pmid": "29624378",
                    "pmcid": null,
                    "type": [
                        "Primary"
                    ],
                    "version": "1.1",
                    "note": null,
                    "metadata": {
                        "title": "MoFi: A Software Tool for Annotating Glycoprotein Mass Spectra by Integrating Hybrid Data from the Intact Protein and Glycopeptide Level",
                        "abstract": "© 2018 American Chemical Society.Hybrid mass spectrometry (MS) is an emerging technique for characterizing glycoproteins, which typically display pronounced microheterogeneity. Since hybrid MS combines information from different experimental levels, it crucially depends on computational methods. Here, we describe a novel software tool, MoFi, which integrates hybrid MS data to assign glycans and other post-translational modifications (PTMs) in deconvoluted mass spectra of intact proteins. Its two-stage search algorithm first assigns monosaccharide/PTM compositions to each peak and then compiles a hierarchical list of glycan combinations compatible with these compositions. Importantly, the program only includes those combinations which are supported by a glycan library as derived from glycopeptide or released glycan analysis. By applying MoFi to mass spectra of rituximab, ado-trastuzumab emtansine, and recombinant human erythropoietin, we demonstrate how integration of bottom-up data may be used to refine information collected at the intact protein level. Accordingly, our software reveals that a single mass frequently can be explained by a considerable number of glycoforms. Yet, it simultaneously ranks proteoforms according to their probability, based on a score which is calculated from relative glycan abundances. Notably, glycoforms that comprise identical glycans may nevertheless differ in score if those glycans occupy different sites. Hence, MoFi exposes different layers of complexity that are present in the annotation of a glycoprotein mass spectrum.",
                        "date": "2018-05-01T00:00:00Z",
                        "citationCount": 14,
                        "authors": [
                            {
                                "name": "Skala W."
                            },
                            {
                                "name": "Wohlschlager T."
                            },
                            {
                                "name": "Senn S."
                            },
                            {
                                "name": "Huber G.E."
                            },
                            {
                                "name": "Huber C.G."
                            }
                        ],
                        "journal": "Analytical Chemistry"
                    }
                }
            ],
            "credit": [
                {
                    "name": "Wolfgang Esser-Skala",
                    "email": "wolfgang.esser-skala@plus.ac.at",
                    "url": "https://wolfgang.esser-skala.at",
                    "orcidid": "https://orcid.org/0000-0002-7350-4045",
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                    "typeEntity": "Person",
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                        "Primary contact"
                    ],
                    "note": null
                }
            ],
            "community": null,
            "owner": "wolfgang.esser-skala",
            "additionDate": "2021-10-12T14:08:00.659281Z",
            "lastUpdate": "2021-10-12T14:15:34.971531Z",
            "editPermission": {
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            },
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            "homepage_status": 0,
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            "confidence_flag": null
        },
        {
            "name": "MULTICOM2",
            "description": "MULTICOM2 is an open-source protein structure prediction system powered by deep learning and distance prediction.",
            "homepage": "https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0",
            "biotoolsID": "multicom2",
            "biotoolsCURIE": "biotools:multicom2",
            "version": [],
            "otherID": [],
            "relation": [],
            "function": [
                {
                    "operation": [
                        {
                            "uri": "http://edamontology.org/operation_0476",
                            "term": "Ab initio structure prediction"
                        },
                        {
                            "uri": "http://edamontology.org/operation_0477",
                            "term": "Protein modelling"
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