VivaxGEN

VivaxGEN provides genotyping data management and population genetics analyses for Plasmodium vivax using short tandem repeat (STR) fragment data to support inference of transmission dynamics.

Key Features:

• Data Repository: Centralized storage for raw genotyping data produced by capillary electrophoresis in Fragment Size Analysis (FSA) file format.
• Standardized Allele Calling Tools: Fragment analysis and standardized allele calling for accurate STR genotyping of Plasmodium vivax.
• Advanced Query System: Filtering, selection, and differentiation of samples and alleles based on user-specified criteria.
• Population Genetic Analyses: Calculation of population differentiation (FST), expected heterozygosity (HE), linkage disequilibrium (IAS), neighbor-joining analysis, and Principal Coordinate Analysis.
• Data Export and Compatibility: Formatting and export of datasets for GENEPOP, Arlequin, and STRUCTURE.
• Global Data Sharing: Aggregation and comparative use of STR genotyping datasets across multiple countries and endemic settings.

Scientific Applications:

• Transmission dynamics of Plasmodium vivax: Analysis of genetic diversity and population structure to inform studies of transmission and control.
• Comparative population genetics: Cross-regional and cross-study comparisons of STR genotypes for surveillance and epidemiological inference.
• Cross-species application: Use of the same genotyping and analysis approaches for related organisms such as Plasmodium falciparum.

Methodology:

Stores FSA files from capillary electrophoresis, performs fragment analysis and standardized allele calling on STR data, supports filtering and selection of samples/alleles, computes FST, expected heterozygosity (HE) and linkage disequilibrium (IAS), conducts neighbor-joining and Principal Coordinate Analysis, and exports datasets formatted for GENEPOP, Arlequin, and STRUCTURE.