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- About -

What is ZooPhy?

ZooPhy is a public health informatics application for phylogeography of zoonotic RNA viruses.

Who is it intended for?

The intended users of ZooPhy are health agencies, agriculture agencies, wildlife agencies, and any other researcher interested in surveillance of zoonotic diseases in either animals or humans.

I am not any of those. Can I still use ZooPhy?

Yes, ZooPhy is 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.

- Functionality -

What can I use ZooPhy for?

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 Given a particular geographical area and timeframe:
  • For a particular virus, what was the migration path?
  • What factors such as climate, population, vaccination, etc. support or protect against virus spread?

Can I use my own data?

Yes. You may upload your own sequences as a .FASTA file.
The .FASTA file needs to be a new line delimited .txt file. The current search limit is 2500 sequences.

Please structure your definition lines as such:

>[ID]|[GeonamesID or LocationName]|[Date]
Where, ID = Some unique ID
GeonamesID = the unique geonames.org ID of your location or location name
Date = the decimal day (2011.83) or year of your sample (2011) or date in format DD-mmm-YYYY (08-Oct-2011)

For example:
>1|5308655|2006.23
ATGGAGAAAATAGTGC...
>2|Phoenix, Arizona|2008.01
ATGGAGAAAATAGTGC..."

What are its functions and features?

ZooPhy can do the following functions:

  • Retrieval of DNA sequences and metadata on zoonotic RNA viruses

  • Multiple sequence alignment (via MAFFT)

  • Bayesian phylogeographic estimation (via BEAST)

  • Visualization of virus migration (via SpreaD3, ZooPhy-Viz)

Result video for spread of Ebola virus in Liberia from 2013 to 2015.

- Database -

Number of Records in the ZooPhy Database

Number of normalized Locations in the ZooPhy Database

Number of normalized Hosts in the ZooPhy Database

- Citation -

How can I cite ZooPhy?

Original Paper:

  • 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.

Papers using ZooPhy:

  • Tahsin T, Weissenbacher D, Jones-Shargani D, et al. Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research. Database (Oxford). 2017;2017:bax093. Published 2017 Dec 28. doi:10.1093/database/bax093
  • Scotch M, Lam TT, Pabilonia KL, Anderson T, Baroch J, Kohler D, DeLiberto TJ. Diffusion of influenza viruses among migratory birds with a focus on the Southwest United States. Infect Genet Evol, 2014. 26: p. 185-93.
  • 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.
  • Scotch M, Mei C, Makonnen YJ, Pinto J, Ali A, Vegso S, Kane M, Sarkar IN, Rabinowitz P. Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt. BMC Genomics. 2013 Dec 10;14:871.

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