ZooPhy - Phylogeography for Zoonotic Disease Surveillance

About ZooPhy

ZooPhy is a public health informatics application for phylogeography of zoonotic RNA viruses . The intended users of ZooPhy are health agencies, agriculture agencies, wildlife agencies, and any other researcher interest in surveillance of zoonotic diseases in either animals or humans. Phylogeography of viruses, such as zoonotic viruses (animal-human transmission) can support public health and disease surveillance. For example, it can help epidemiologists answer questions such as ‘For a particular geographical area and timeframe:

  • Which animal hosts most impact virus propagation?
  • For a particular virus, what was the migration path?
  • Where is it going?
  • What was the trend of the estimated viral population within a specific animal host?

Once it is live, ZooPhy will be freely available to the public with the hope that it will help enhance population surveillance of human and animal zoonotic diseases and inform public health decision making.


ZooPhy can do the following functions:

  • Bayesian phylogeographic trees
  • ZooPhy includes its own webservice for Bayesian Evolutionary Analysis by Sampling Trees (BEAST) to produce different models of evolution.
  • Bayesian skyline plots
  • Through BEAST, ZooPhy can produce Bayesian skyline plots for analysis of population genetics and estimates of viral population over time.
  • Multiple sequence alignment
  • ZooPhy utilizes a webservice to connect to Clustal to perform alignment of nucleotide or amino acid sequences.
  • Evaluation of substitution models

Citing ZooPhy

The publications related to ZooPhy are:

  • Scotch M, Mei C, Brandt C, Sarkar IN, Cheung K. At the intersection of public-health informatics and bioinformatics: using advanced Web technologies for phylogeography. Epidemiology. 2010 Nov;21(6):764-8.
  • Scotch M, Mei C. Phylogeography of swine influenza H3N2 in the United States: translational public health for zoonotic disease surveillance. Infect Genet Evol. 2013 Jan;13:224-9.