https://github.com/dreamalligator/petrie

a Graph-based phylogenetic tree, implemented in Javascript.
https://github.com/dreamalligator/petrie

algorithms data-structures graph nature petrie phylogeny taxonomy tree

Last synced: 26 days ago
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a Graph-based phylogenetic tree, implemented in Javascript.

• Host: GitHub
• URL: https://github.com/dreamalligator/petrie
• Owner: dreamalligator
• Created: 2018-05-28T20:44:20.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2018-06-16T20:12:37.000Z (over 6 years ago)
• Last Synced: 2024-11-30T01:49:40.256Z (about 2 months ago)
• Topics: algorithms, data-structures, graph, nature, petrie, phylogeny, taxonomy, tree
• Language: JavaScript
• Homepage:
• Size: 40 KB
• Stars: 1
• Watchers: 0
• Forks: 0
• Open Issues: 4
• Metadata Files:
  • Readme: README.md

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README

        
# Petrie

![petrie](https://github.com/nebulousdog/petrie/blob/master/petrie.png)

![vulnerabilities](https://snyk.io/test/github/nebulousdog/petrie/badge.svg?targetFile=package.json)

![coverage](https://coveralls.io/repos/github/nebulousdog/petrie/badge.svg?branch=master)

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](https://github.com/nebulousdog/petrie/issues).

## Getting started

Install package.

```bash

yarn add petrie

```

Import module.

```javascript

import Tree from 'petrie';

```

Create a cached tree from the ICPS [Carnivorous Plant Names Database](http://cpnames.carnivorousplants.org/).

```javascript

```

Create a cached tree using NCBS.

```javascript

```

Creating your own tree.

```javascript

```

Import your data.

```javascript

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

```

Initialize a new `Tree` instance.

```javascript

const tree = new Tree(data);

```

Searching.

```javascript

tree.find('nepenthes');

tree.find('nepenthes a');

```

Taxonomy

```javascript

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

```javascript

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.

```javascript

```

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.

```javascript

import d3 from 'd3';

```

## Contributing

Issues and pull requests are very welcome!

### Tests

`yarn test`

## License

MIT