Alitreeviz NPM

alitreeviz

Be careful, this a very preliminary version that could contain bugs.

Visualisation of multiple sequence alignments and phylogenetic trees.

Screenshot

Features

Does not need any server
Display phylogenetic tree (newick format)
Display multiple sequence alignment (MSA) (multifasta format)
Display MSA overview
Select sequences in the MSA from the phylogenetic tree (the names of the sequences must correspond)
Display position tracks above the MSA overview and detailed view (text file with one position per row)

Usage

Test official instance

Here : https://lipm-browsers.toulouse.inrae.fr/alitreeviz/

From git repository

You need npm installed on your computer

git clone https://github.com/lipme/alitreeviz.git

Project setup

npm install

Compiles and hot-reloads for development

npm run serve

Now you can use alitreeviz directly since it does not require any server.

Compiles and minifies for production

npm run build

In Vue project (vue 2 compatible)

npm install --save alitreeviz

<template>
	<alitreeviz />
</template>
<script>
import Alitreeviz from './views/Alitreeviz.vue'
import 'alitreeviz/dist/alitreeviz.css'


export default {
  name: 'App',

  components: {
    Alitreeviz
  }
}
</script>

Note: For the moment, I don't know why, margins might be added so that the component becomes centered in the page...