patristic

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

• Parse newick into Javascript objects representing the phylogenetic tree
• Run rapid neighbor joining to compute a phylogenetic tree from a distance matrix
• Infer a patristic distance matrix from a phylogenetic tree
• Reroot a tree on any given Branch
• Infer directionality between two Branches in the tree
• ...And quite a bit more.

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

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.

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:

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.

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. 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 and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/privacy.html.

Contributing

Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) 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 or later.

All comments, messages, pull requests, and other submissions received through CDC including this GitHub page are subject to the Presidential Records Act and may be archived. Learn more at 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.

Notices

Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.

Updates

Resolve backward branches