patristic/README.md

Patristic Inference library for Node and Browser

# patristic

`patristic` is a javascript toolkit for working with phylogenies. It can:

* [Parse newick](https://cdcgov.github.io/patristic/docs/#parsenewick) into
[Javascript objects representing the phylogenetic tree](https://cdcgov.github.io/patristic/docs/#branch)
* Run [rapid neighbor joining](http://pure.au.dk/ws/files/19821675/rapidNJ.pdf)
to [compute a phylogenetic tree from a distance matrix](https://cdcgov.github.io/patristic/docs/#parsematrix)
* [Infer a patristic distance matrix](https://cdcgov.github.io/patristic/docs/#tomatrix)
from a phylogenetic tree
* [Reroot a tree on any given Branch](https://cdcgov.github.io/patristic/docs/#reroot)
* [Infer directionality between two Branches in the tree](https://cdcgov.github.io/patristic/docs/#sources)
* [...And quite a bit more.](https://cdcgov.github.io/patristic/docs/#table-of-contents)

## Installation

To install patristic with NPM use: `npm install --save patristic`

## Usage

Please note that this is a beta-stage API and may change (possibly dramatically)
in the very near future.

### Quick Start

```javascript
var newick = "(A:0.1,B:0.2,(C:0.3,(D:0.4,E:0.6):0.1):0.5);";
var tree = patristic.parseNewick(newick);
```

We can use this tree to compute a patristic distance matrix.

```javascript
var matrix = tree.toMatrix();
```

Note that elements in the tree object maintain references to their parents,
creating circular references. If you need a tree without circular references for
serialization:

```javascript
tree.toObject();
```

(`tree.toJSON` aliases that, so you can `JSON.stringify` a Branch and it just
works. 😉)

For more details, check out our [Full Documentation](https://cdcgov.github.io/patristic/docs/#table-of-contents).

## Public Domain
This repository constitutes a work of the United States Government and is not
subject to domestic copyright protection under 17 USC § 105. This repository is in
the public domain within the United States, and copyright and related rights in
the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/).
All contributions to this repository will be released under the CC0 dedication. By
submitting a pull request you are agreeing to comply with this waiver of
copyright interest.

## License
The repository utilizes code licensed under the terms of the Apache Software
License and therefore is licensed under ASL v2 or later.

This source code in this repository is free: you can redistribute it and/or
modify it under the terms of the Apache Software License version 2, or (at your
option) any later version.

This source code in this repository is distributed in the hope that it will be
useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software
License for more details.

You should have received a copy of the Apache Software License along with this
program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html

The source code forked from other open source projects will inherit its license.

## Privacy
This repository contains only non-sensitive, publicly available data and
information. All material and community participation is covered by the
Surveillance Platform [Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)
and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).
For more information about CDC's privacy policy, please visit [http://www.cdc.gov/privacy.html](http://www.cdc.gov/privacy.html).

## Contributing
Anyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo)
and submitting a pull request. (If you are new to GitHub, you might start with a
[basic tutorial](https://help.github.com/articles/set-up-git).) By contributing
to this project, you grant a world-wide, royalty-free, perpetual, irrevocable,
non-exclusive, transferable license to all users under the terms of the
[Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or
later.

All comments, messages, pull requests, and other submissions received through
CDC including this GitHub page are subject to the [Presidential Records Act](http://www.archives.gov/about/laws/presidential-records.html)
and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).

## Records
This repository is not a source of government records, but is a copy to increase
collaboration and collaborative potential. All government records will be
published through the [CDC web site](http://www.cdc.gov).

## Notices
Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)
for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),
[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),
and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).

## Updates
Resolve backward branches