This is the home page for Core Hunter, the genetic resource sampling software.
Core Hunter is a program that can be used for sampling genetic resources from a reference data set. Users can specify the sampling intensity and which genetic measures will be used for selection criteria. For instance, a core subset could be selected that best maximizes the average modified Rogers' distance, or one that maximizes the Shannon's diversity index. Users can also maximize multiple genetic measures simultaneously, by specifying a weight for each required measure. The program is run from the command line and has been tested on Linux, Mac OS X (PPC/Intel), and Microsoft Windows XP/Vista.
A README file is provided with the software to get a user started immediately. For a more in depth description of the program, its options, supported data formats, and general usage instructions refer to the Core Hunter Quick Start Guide.
Core Hunter Software
Core Hunter Source Code
- The source code for core hunter will be release upon successful publication.
Example data sets
- bulk data set: obtained by fingerprinting 275 bulks (populations represented by two bulks of 15 genotypes each) of maize landrace populations from the Americas and Europe, using 24 SSR markers with at least one SSR per chromosome and a total of 186 alleles (Dubreuil
et al., 2006).
- accession data set: obtained by fingerprinting 521 maize individuals from 25 maize populations using 26 SSR markers with at least one SSR per chromosome and a total of 209 alleles (Warburton et al., 2004).
- populations data set: obtained from the 'accession data set' by grouping the individuals of each population, and calculating the allele frequency per population; this data set had a total of 25 populations and 209 alleles (Warburton et al., 2004).
Core subsets generated by Core Hunter in the Core Hunter paper: