Web app for visualizing pathogen evolution

Build Status NPM version License: AGPL v3

Introduction

Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread. Our goal is to aid epidemiological understanding and improve outbreak response.

Resulting data and inferences are available live at the website nextstrain.org. Documentation is available at nextstrain.org/docs.

Auspice

Definition: Observation by an augur, ie a prophetic sign.

Auspice is an open-source interactive web app for visualizing phylogenomic data. It may be used in tandem with augur or on its own. It may be used to look at phylogenetic trees on your own computer or may be used as a server to share results broadly.

Please see nextstrain.github.io/auspice for auspice documentation.

Installation

npm install -g auspice

See here for more details.

Running Auspice

auspice view starts the server, which makes local datasets available in a browser at localhost:4000/local.

By default, the datasets are sourced from the current working directory (or an auspice subfolder if it exists). Please run auspice view -h to see how to change this directory, as well as the directory where narratives are sourced from.

License and copyright

Copyright 2014-2019 Trevor Bedford and Richard Neher.

Source code to Nextstrain is made available under the terms of the GNU Affero General Public License (AGPL). Nextstrain 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 GNU Affero General Public License for more details.