VNTR DIversity and Confidence Extractor                 For information on how to use this service please README

Generate the Simpsons and Hunter-Gaston Diversity Indices for a VNTR dataset

A Diversity Index (DI), when applied to VNTR data, is a measure of the variation of the number of repeats at each locus. It can range from zero (no diversity) to one (extreme diversity). i.e. Loci with a similar number of repeats in each sample will have a lower DI, whereas a locus where the number of repeats is different for nearly every sample will have a very high DI.

The Hunter-Gaston estimate of diversity incorporates a finite sample adjustment which is generally desirable. It is very similar to Simpsons when the sample size is above 50 or diversity is less than 90%.

There is often a degree of uncertainty associated with the DI (as with any statistical value), therefore Confidence Intervals (CI) are also generated for each of the loci examined by this tool. A CI gives the precision of the DI by providing the upper and lower boundaries.

A high DI with a narrow CI indicates accurate measurement of a highly variable locus. These loci may be sufficiently variable to be used as an indicator to discriminate between samples or as a starting point for assay developement.

Additional information

Although originally developed for VNTR data, V-DICE can analyse any list of information presented in the CSV format, including MLST and SBT profiles.
Even non-numerical text lists can be analysed however graph axis labels are not optimised for this.

If you have any questions or comments about this tool, contact the author
  Paste or upload your dataset in CSV (comma separated) format:

A sample dataset can be downloaded here

A BioNumerics script is available that exports character data in the appropriate format.
To enable the script, simply download it to your BioNumerics script folder.