phylotree/bin/phylotree-neighbor-join.js

A JavaScript library for developing applications and interactive visualizations involving [phylogenetic trees](https://en.wikipedia.org/wiki/Phylogenetic_tree), written as an extension of the [D3](http://d3js.org) [hierarchy layout](https://github.com/d3/

#!/usr/bin/env node

const fs = require("fs"),
  phylotree = require("../dist/phylotree.js"),
  commander = require("commander"),
  _ = require("lodash");

commander
  .arguments("<fasta>", "Input fasta file")
  .usage("./test/data/CD2.fas")
  .on("--help", function() {
    console.log("\nConstructs neighbor-joining algorithm");
  })
  .parse(process.argv);


fs.readFile(commander.args[0], ( err, fastaData ) => {

	let fasta = phylotree.parseFasta(fastaData);
	let nodeList = _.keys(fasta);
	let distanceMatrix = phylotree.getDistanceMatrix(fasta);
	let distanceMatrixArr = _.values(distanceMatrix);

	let nj = phylotree.neighborJoining(distanceMatrixArr, _.keys(fasta).length, nodeList)
	console.log(nj.getNewick());

});