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What is VivaxGEN?

Molecular analysis of Plasmodium vivax has potential to provide important information on the transmission dynamics of the parasites. The VivaxGEN platform was developed to support the population genetic analyses by providing a framework for collating, analyzing and sharing P. vivax short tandem repeat data.

The platform provides a repository for raw data generated by capillary electrophoresis (FSA files), with fragment analysis and standardized allele calling tools. Using the query system users can filter, select and differentiate samples and alleles based on specified criteria.

Key population genetic analyses are supported including measures of population differentiation (FST), multiplicity of infection (MOI), expected heterozygosity (HE), linkage disequilibrium (IAS), neighbor-joining analysis and Principal Coordinate Analysis.

Datasets can also be formatted and exported for application in commonly used population genetic software including GENEPOP, Arlequin and STRUCTURE.

Users can work on private datasets by logging into the system with their username and password. To set up a new account, please contact the Systems Administrator: anto@eijkman.go.id. Publicly available data sets can be explored without an account by selecting the Enter as Anonymous User option.

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