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Software to map genomics of disease outbreaks

Published online 28 April 2014

Biplab Das

A new desktop application can visualize genomic data from populations of pathogens in real-time. Known as SVAMP (sequence variation analysis, maps and phylogeny), the software can create maps with colour coded isolates based on the country of origin and chart the phylogenetic tree of the parasite.

"This software can be employed to investigate outbreaks as long as samples from the outbreaks are sequenced and the resulting data, after mapping to reference genome, is made available to the software," says Arnab Pain, of King Abdullah University of Science and Technology, Saudi Arabia, and a senior co-author of the study published in the journal Bioinformatics1.

The programme was tested using two previously published data sets on methicillin-resistant Staphylococcus aureus (MRSA) bacteria and the malaria parasite Plasmodium falciparum. The MRSA data contained 63 MRSA isolates from 15 countries, while the malaria parasite data consisted of 245 samples from Africa, Southeast Asia and Papua New Guinea.

The researchers say it can be used to study naturally occurring genetic mutations, population structure and geographical variability of pathogens in environments. The software was able to construct the phylogenetic tree of 63 MRSA isolates in 20 seconds.


  1. Naeem, R. et al. SVAMP: Sequence variation analysis, maps and phylogeny. Bioinformatics (2014) doi:10.1093/bioinformatics/btu176