https://github.com/veg/alignment.js

Javascript alignment viewer
https://github.com/veg/alignment.js

Last synced: 4 months ago
JSON representation

Javascript alignment viewer

• Host: GitHub
• URL: https://github.com/veg/alignment.js
• Owner: veg
• License: mit
• Created: 2018-01-17T21:30:57.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2023-11-29T20:50:31.000Z (7 months ago)
• Last Synced: 2024-02-24T22:03:06.340Z (4 months ago)
• Language: JavaScript
• Size: 14.1 MB
• Stars: 6
• Watchers: 6
• Forks: 7
• Open Issues: 28
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• awesome-genome-visualization - alignment.js
• repo-5916-awesome-genome-visualization - alignment.js - genome-visualization/alignmentjs.png) (MSA)

README

        
# alignment.js

A suite of reusable [React](http://reactjs.org/) components for creating a variety of visualizations involving [multiple sequence alignments](https://en.wikipedia.org/wiki/Multiple_sequence_alignment). [View the live demo here](http://alignment.hyphy.org/).

`alignment.js` can be used to create standard MSA viewers, utilizing functional programming to permit custom behavior such as highlighting individual sites:

![alt text](images/standard.png)

as well as scaffold viewers for next-generation sequencing data where a reference sequence stays fixed to the top:

![alt text](images/scaffold.gif)

and joint phylogeny/alignment viewers using packages like [phylotree.js](https://github.com/veg/phylotree.js):

![alt text](images/phyalign.png)

## Installation

`alignment.js` is [available on NPM](https://www.npmjs.com/package/alignment.js) and can thus be installed with `npm`

```

npm install alignment.js

```

or `yarn`

```

yarn add alignment.js

```

## Development

### Installation

```

git clone https://github.com/veg/alignment.js

cd alignment.js

yarn

```

### Application

Start the development server:

```

yarn develop

```

`webpack-dev-server` will find an available port and open up your default browser. Refreshes will automatically occur on writes to files.

### Library

For testing the library in dependent packages before releases, `alignment.js` uses yalc. The library is built by Babeling `src` into `lib`, and `lib` is published. For convenience, this is encapsulated in the following NPM script:

```

yarn yalc

```

### Publishing

```

yarn library

cd lib

npm publish

```

## Deployment

### Application

Server will read from environment variable `$PORT`.

```

yarn app

yarn serve

```