Nth Permutation Mathematics

    neighbor-joining

    1.0.4 • Public • Published

    Neighbor-joining is an NPM package for creating phylogenetic trees. It bases on Rapid Neighbour-Joining algorithm.

    Installation

    To install Neighbor-joining package with NPM use: npm install neighbor-joining

    Usage

    var RNJ = new RapidNeighborJoining(D, taxa, copyDistanceMatrix, taxonIdAccessor);

    Description of arguments used in initialization:

    • D - distance matrix (two dimensional array of size NxN)
    • taxa - array of size N with taxa data (such as strings or objects). Element (taxon) at first index corresponds to first row/column of the distance matrix and so on.
    • copyDistanceMatrix - flag specifying whether D can be modified or must be copied. Copying might minimally increase the initialization time. Default: false.
    • taxonIdAccessor - function for retrieving the name/identifier of a taxon. It is only called during Newick tree creation. Default: function(t){ return t.name }.

    Example

    var D = [
        [0,  5,  9,  9, 8],
        [5,  0, 10, 10, 9],
        [9, 10,  0,  8, 7],
        [9, 10,  8,  0, 3],
        [8,  9,  7,  3, 0]
    ];
    var taxa = [
        {
            name: "A",
            genotype: "g1"
        },
        {
            name: "B",
            genotype: "g2"
        },
        {
            name: "C",
            genotype: "g3"
        },
        {
            name: "D",
            genotype: "g4"
        },
        {
            name: "E",
            genotype: "g5"
        }
    ];
    var RNJ = new RapidNeighborJoining(D, taxa);
    RNJ.run();
    var treeObject = RNJ.getAsObject();
    var treeNewick = RNJ.getAsNewick();

    Then, treeObject will contain the following object:

    {
        "taxon": null,
        "length": null,
        "children": [{
            "taxon": {
                "name": "C",
                "genotype": "g3"
            },
            "length": 2,
            "children": []
        }, {
            "taxon": null,
            "length": 2,
            "children": [{
                "taxon": null,
                "length": 3,
                "children": [{
                    "taxon": {
                        "name": "A",
                        "genotype": "g1"
                    },
                    "length": 2,
                    "children": []
                }, {
                    "taxon": {
                        "name": "B",
                        "genotype": "g2"
                    },
                    "length": 3,
                    "children": []
                }]
            }, {
                "taxon": null,
                "length": 2,
                "children": [{
                    "taxon": {
                        "name": "D",
                        "genotype": "g4"
                    },
                    "length": 2,
                    "children": []
                }, {
                    "taxon": {
                        "name": "E",
                        "genotype": "g5"
                    },
                    "length": 1,
                    "children": []
                }]
            }]
        }]
    }

    treeNewick will keep the following string:

    "(C:2,((A:2,B:3):3,(D:2,E:1):2):2);"

    Install

    npm i neighbor-joining

    DownloadsWeekly Downloads

    5

    Version

    1.0.4

    License

    MIT

    Last publish

    Collaborators

    • maciejkorzepa