dreamalligator/petrie

a Graph-based phylogenetic tree, implemented in Javascript.

Petrie

a Graph-based phylogenetic tree, implemented in Javascript.

Phylogeny and Taxonomy

Whether your purposes are phylogenetic or taxonomic in nature doesn't matter. That is, whether you are making a evolutional tree, or a species classification tree. Your source of graph data will determine the utility.

• https://en.wikipedia.org/wiki/Phylogenetic_tree
• https://en.wikipedia.org/wiki/Taxonomic_rank

Graph

• https://github.com/trekhleb/javascript-algorithms/tree/master/src/data-structures/graph

Implementation

todo

Nepenthes Example

I chose Nepenthes, because I grow them at home! This project is part of a bigger one related to carnivorous plants and terraria that I'm breaking apart.

• http://www.carnivorousplants.org/cp/evolution/Nepenthes

I'm a hobbiest, so if youre actually in a scientific field and have favorite phylogenetic database, data structure, protocol to share this kind of data, or other research I know nothing about!, I'd love to hear about it in the issues.

Getting started

Install package.

yarn add petrie

Import module.

import Tree from 'petrie';

Create a cached tree from the ICPS Carnivorous Plant Names Database.

Create a cached tree using NCBS.

Creating your own tree.

Import your data.

import data from './data'; // default export location

Initialize a new Tree instance.

const tree = new Tree(data);

Searching.

tree.find('nepenthes');

tree.find('nepenthes a');

Taxonomy

const ampullaria = tree.find('nepenthes ampullaria')[0];

ampullaria.name // binomial name
ampullaria.domain
ampullaria.order
ampullaria.species

ampullaria.divisions // synonymous with Species.prototype.children
ampullaria.order.divisions

// using HAMT methods to determine parents and children
ampullaria.children
const nepenthes = tree.find('nepenthes')[0]
ampullaria.isParent(nepenthes);
// false
nepenthes.isParent(ampullaria);
// true

Phylogeny

const nepenthes
ampullaria.geneticDistance();

HAMT

Using HAMT means that we have an entire tree-searching algorithm at our hands. Let's use it to create a binomial name searching autocomplete.

Graphing

D3 is an optional dependency to try to keep this project footprint small, and because not everybody needs graphing. If you like other chart libraries, please feel free to let me know in the issues.

import d3 from 'd3';

Contributing

Issues and pull requests are very welcome!

Tests

yarn test

License

MIT

petrie's Issues

graphical example

provide a d3 example

ITIS database examples

• show single species example
• show full database example

base metadata and extension

decide on base metadata, and method of extending.

schema validation

• provide input/output validation for Petrie
• break out the validator for input, so that anyone wishing to write an API wrapper to input taxonomic data to Petrie can use the same schema and tests as everyone else.
  • add example usage to Petrie ITIS

example JS validators:

• https://github.com/hapijs/joi
• https://github.com/ansman/validate.js/