hzi-bifo / sdplots

This repository contains all published data.

SDplots

This repository contains all data that is published in the manuscript 'Sweep Dynamics (SD) plots: Computational identification of selective sweeps to monitor the adaptation of influenza A viruses' and a docker instance of the SD plots pipeline.

The pre-print of this study is available under http://biorxiv.org/content/early/2017/02/21/110528

Data

The Data folder contains all data that was used in the publication. We provide the sequence alignments, phylogenetic trees and SD plots statistics for each protein that we analyzed. Also, the protein structures are available.

Figures&Tables

This folder comprises the figures and tables that are published in the manuscript and additional information that is not included in the manuscript.

Software

In here, we supply the SD plots software. Detailed descriptions and instructions are provided in the readme https://github.com/hzi-bifo/SDplots/blob/master/Software/README.md .

sdplots's Issues

Can SDplots be used to map other subtypes of influenza?

Hi, @alicemchardy
Can SDplots be used to map other subtypes of influenza? Like bird flu.
I can run the demo data but not my data.
Error: the following invalid characters have been detected in file HA_cds.fa:
Was the input sequence dataset download from GISAID?