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Read, write, and manipulate phylogenetic trees

License: MIT License

Dhall 5.30% PureScript 79.67% JavaScript 3.77% TypeScript 11.26%

phylogenetic-trees newick purescript typescript nhx nexus phyloxml nexml

phylio's Introduction

Phylio

Read, write, and manipulate phylogenetic trees.

Supported formats are:

PhyloXML
Newick with support for NHX and Extended Newick
NEXUS

Installation

For javascript projects using NPM:

npm i --save @vibbioinfocore/phylio

For javascript projects using yarn:

yarn add @vibbioinfocore/phylio

For Purescript projects:

spago install purescript-phylio

Usage

From Javascript:

import { parse } from '@vibbioinfocore/phylio';

try {
    const tree = parse("(A,B)C;");
} catch (Error e) {
    console.log(e);
}

From Purescript:

import Bio.Phylogeny (parseNewick)

tree = parseNewick "(A,B)C;"

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

Please make sure to update/add tests as appropriate.

License

MIT

phylio's People

Contributors

Stargazers

Watchers

phylio's Issues

Read for NeXML formatted data

Read for PhyloXML formatted data

Dependency Dashboard

This issue lists Renovate updates and detected dependencies. Read the Dependency Dashboard docs to learn more.

Warning

These dependencies are deprecated:

Datasource	Name	Replacement PR?
npm	`eslint-plugin-node`

Rate-Limited

These updates are currently rate-limited. Click on a checkbox below to force their creation now.

Open

These updates have all been created already. Click a checkbox below to force a retry/rebase of any.

Detected dependencies

github-actions

.github/workflows/test.yml

actions/checkout v3

actions/setup-node v3

npm

package.json

@typescript-eslint/eslint-plugin 5.62.0

@typescript-eslint/parser 5.62.0

ava 5.2.0

esbuild 0.17.18

eslint 8.40.0

eslint-config-prettier 8.8.0

eslint-plugin-import 2.27.5

eslint-plugin-node 11.1.0

eslint-plugin-promise 6.1.1

npm-dts 1.3.12

prettier 2.8.8

purescript 0.15.9

purs-backend-es 1.3.2

purs-tidy 0.9.3

spago ^0.21.0

ts-node 10.9.1

tsx ^3.12.7

typescript 5.0.4

Check this box to trigger a request for Renovate to run again on this repository

Support RecPhyloXML

http://phylariane.univ-lyon1.fr/recphyloxml/

Support some ad-hoc Newick extensions

e.g. Wikipedia documents :[bootstrap]:[prob] as additional fields on a node.

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