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trvrb committed Jul 3, 2018
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## Live website
## Current status
nextflu is live at [nextflu.org](https://nextflu.org).
_All Nextflu development has been folded into the Nextstrain project. Python build pipine is available at [nextstrain/augur](https://github.com/nextstrain/augur) (which supercedes build pipeline in `blab/nextflu/augur`) and JavaScript visualization is available at [nextstrain/auspice](https://github.com/nextstrain/auspice) (which supercedes visualization in `blab/nextflu/auspice`)._
_Live display of seasonal flu evolution is available at [nextstrain.org/flu](http://nextstrain.org/flu)._
## Introduction
nextflu is designed to perform near real-time tracking of influenza virus evolution. The current version of nextflu is focused on tracking seasonal influenza evolution in humans, looking at sequences from the hemagglutinin (HA) gene. It's divided into two components:
* _augur_, which takes a `.fasta` file of flu sequences and builds an annotated phylogeny
* _auspice_, which displays this annotated phylogeny in an interactive web-based visualization
Augur build scripts are housed at [nextstrain/augur](https://github.com/nextstrain/augur). These produce a series of JSON files that are displayed interactively on the web. Currently, the same JSONs produced by augur can be displayed with auspice v1 housed in [this repo](auspice/) or with auspice v2 housed at [nextstrain/auspice](https://github.com/nextstrain/auspice). Auspice v1 is live at [nextflu.org](https://nextflu.org) and auspice v2 is live at [nextstrain.org/flu](http://nextstrain.org/flu). Auspice v1 still provides greater functionality for influenza, but the intention is to eventually migrate to auspice v2.
Augur build scripts are housed at [nextstrain/augur](https://github.com/nextstrain/augur) and auspice visualization tool is housed at [nextstrain/auspice](https://github.com/nextstrain/auspice). Legacy v1 versions of both `augur` and `auspice` are maintained in this repository for purposes of posterity.
## Citation

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## Auspice
Website for visualizing and interacting with phylogenies produced by the [nextstrain/augur](https://github.com/nextstrain/augur) pipeline. Interactive visualization is done with [d3.js](http://d3js.org/). This is v1 of auspice and is in maintenance mode. Active development is continuing on v2 of auspice at [nextstrain/auspice](https://github.com/nextstrain/auspice).
_Note: As of Sep 2017, this JavaScript app is deprecated in favor of [nextstrain/auspice](https://github.com/nextstrain/auspice). The code in this directory is kept in place for archival reasons._
Website for visualizing and interacting with phylogenies produced augur pipeline. Interactive visualization is done with [d3.js](http://d3js.org/).
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