ViralNet: Program for Computing Network Structures in RNA Viral Populations


ViralNet is an application for estimating reticulated structures of mixed viral populations.

The program takes as input a text file containing tables of linkage information and sequencing depth information and outputs possible reticulated networks, sets of haplotypes and clonal prevalences.

Examples of input files of both real data, and example data from [1] are included, along with outputs.

If you use ViralNet, we would appreciate if you could cite [1].


ViralNet is written in C++, and is released under the GNU General Public License, the source code and read me files are freely available here (Download to modify providing the copyright notice remains intact and due credit is given to the authors in publications.

ViralNet is Copyright © 2014 Donatien Fotso & Chris Greenman.


For technical questions or feature requests, e-mail:


[1] Inferring the Clonal Structure of Viral Populations from Time Series Sequencing, Fotso-Chedom D, Murcia PR, and Greenman CD, ArXiv,


This software is supplied as-is, with no warranty of any kind expressed or implied. We have made every effort to avoid errors in design and execution of this software, but we will not be liable for its use or misuse. The user is solely responsible for the validity and consequences of any results generated.

Research Team

Dr. Donatien Fotso-Chedom (TGAC), Dr. Pablo Murcia (MRC-University of Glasgow Centre for Virus Research), Dr. Chris Greenman (CMP)