Neighbor Joining library for NPM.
npm install neighbor-joiningNeighbor-joining is an NPM package for creating phylogenetic trees. It bases on Rapid Neighbour-Joining algorithm.
To install Neighbor-joining package with NPM use: npm install neighbor-joining
``javascript`
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: .function(t){ return t.name }
* taxonIdAccessor - function for retrieving the name/identifier of a taxon. It is only called during Newick tree creation. Default: .
javascript
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,
will contain the following object:
`javascript
{
"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": []
}]
}]
}]
}
`
will keep the following string:
`javascript
"(C:2,((A:2,B:3):3,(D:2,E:1):2):2);"
``