https://github.com/biosustain/neighbor-joining
Rapid Neighbor-Joining phylogenetic tree creation method implementation for Node.js
https://github.com/biosustain/neighbor-joining
neighbor-joining nodejs phylogenetic-trees phylogenetics
Last synced: about 2 months ago
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Rapid Neighbor-Joining phylogenetic tree creation method implementation for Node.js
- Host: GitHub
- URL: https://github.com/biosustain/neighbor-joining
- Owner: biosustain
- Created: 2016-04-14T11:27:02.000Z (about 9 years ago)
- Default Branch: master
- Last Pushed: 2016-07-22T11:26:42.000Z (almost 9 years ago)
- Last Synced: 2025-04-06T10:44:50.048Z (about 2 months ago)
- Topics: neighbor-joining, nodejs, phylogenetic-trees, phylogenetics
- Language: JavaScript
- Homepage:
- Size: 10.7 KB
- Stars: 3
- Watchers: 4
- Forks: 8
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
Neighbor-joining is an NPM package for creating phylogenetic trees. It bases on [Rapid Neighbour-Joining](http://pure.au.dk/ws/files/19821675/rapidNJ.pdf) algorithm.
# Installation
To install Neighbor-joining package with NPM use: `npm install neighbor-joining`
# Usage
```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: `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
```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, `treeObject` 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": []
}]
}]
}]
}
```
`treeNewick` will keep the following string:
```javascript
"(C:2,((A:2,B:3):3,(D:2,E:1):2):2);"
```