gnomic-phylogeny
v1.0.5
Published
Gnomic grammar phylogeny library for NPM
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Gnomic-phylogeny
Gnomic-phylogeny is an NPM package for generating distance matrix or phylogenetic trees based on Gnomic - grammar for describing genotypes and phenotypes of microbial strains.
Installation
To install Neighbor-joining package with NPM use: npm install neighbor-joining
Description
Gnomic-phylogeny operates on gnomic Genotype
objects. It has two main functions:
buildDistanceMatrix(gnomicGenotypes)
- generates two dimensional array containing distances between genotypesbuildPhylogeneticTree(taxa, gnomicGenotypes, newick=false)
- generates a phylogenetic tree as an object or a string in Newick format. First, the function callsbuildDistanceMatrix
function and then it uses Neighbour-joining NPM library to create a phylogenetic tree. To get more
Currently, features and plasmids are distinguished only by looking at their name
property. The following table presents the approach used to calculate the distance between two genotypes.
| | Genotype 1 | Genotype 2 | Distance |
|-----------|:----------:|:----------:|----------|
| feature A | inserted | deleted | 2 |
| | inserted | N/A | 1 |
| | N/A | inserted | 1 |
| | N/A | N/A | 0 |
| | inserted | inserted | 0 |
| | deleted | deleted | 0 |
| plasmid B | inserted | N/A | 1 |
| | N/A | inserted | 1 |
| | N/A | N/A | 0 |
| | inserted | inserted | 0 |
Example
var Genotype = require("gnomic-grammar").Genotype;
var _gnomicPhylogeny = require("gnomic-phylogeny");
var buildDistanceMatrix = _gnomicPhylogeny.buildDistanceMatrix;
var buildPhylogeneticTree = _gnomicPhylogeny.buildDistanceMatrix;
var taxa = [
{ name: "A",
genotype: "p1{geneA geneB}::cc+ geneC>geneD" },
{ name: "B",
genotype: "geneC>geneD" },
{ name: "C",
genotype: "p1{geneA geneF} geneC>geneE" },
{ name: "D",
genotype: "p2{geneG geneC} +geneG" }
];
var gnomicGenotypes = taxa.map(d => d.genotype).map(Genotype.parse);
var D = buildDistanceMatrix(gnomicGenotypes);
var treeObject = buildPhylogeneticTree(taxa, gnomicGenotypes);
var treeNewick = buildPhylogeneticTree(taxa, gnomicGenotypes, true);
As a result, D
, treeObject
and treeNewick
will keep the following information:
D
:
[[0, 1, 2, 5],
[1, 0, 3 ,4],
[2, 3, 0, 5],
[5, 4, 5, 0]]
treeObject
:
{
"taxon": null,
"length": null,
"children": [{
"taxon": null,
"length": 1.75,
"children": [{
"taxon": null,
"length": 0.5,
"children": [{
"taxon": {
"name": "A",
"genotype": "p1{geneA geneB}::cc+ geneC>geneD"
},
"length": 0.5,
"children": []
}, {
"taxon": {
"name": "B",
"genotype": "geneC>geneD"
},
"length": 0.5,
"children": []
}]
}, {
"taxon": {
"name": "C",
"genotype": "p1{geneA geneF} geneC>geneE"
},
"length": 1.5,
"children": []
}]
}, {
"taxon": {
"name": "D",
"genotype": "p2{geneG geneC} +geneG"
},
"length": 1.75,
"children": []
}]
}
treeNewick
:
"(((A:0.5,B:0.5):0.5,C:1.5):1.75,D:1.75);"