Software for rarefaction of private alleles and hierarchical sampling designs




Large genetic samples are expected to have more alleles than small samples. Rarefaction is a statistical technique to deal with this problem so the number of alleles in large samples can be compared with the number of alleles in small samples. The statistical technique was developed in 1971 by Hurlbert to compare the number of species in different ecological samples. HP-Rare performs applies the method to private alleles and hierarchical sampling designs.




Please see the following manuscripts for a description of the method:


Kalinowski ST (2004) Counting alleles with rarefaction: private alleles and hierarchical sampling designs. Conservation Genetics 5:539-543


Kalinowski ST (2005) HP-Rare: a computer program for performing rarefaction on measures of allelic diversity. Molecular Ecology Notes 5:187-189.



Input files

HP-Rare should read GENEPOP files (either 4 or 6 digit format). There are currently two GENEPOP formats. HP-Rare follows the online format--sample names are read by the first individual in the sample. Alternatively, sample names can be placed after the POP delimiter - which may be more convenient.



Hierarchy files

Sampling hierarchies are described in "Hierarchy" files that have the following format:



     Old_Dad     California      O.nelsoni

     Eagle       California      O.nelsoni

     CDome       Arizona         O.nelsoni

     Wheeler     New_Mexico      O.canadensis


The first line of the file lists the name of each level in the hierarchy, from lowest level to highest level. Each label must be separated by at least one space or tab. The left-most column lists the name of the samples contained in the GENEPOP data file. You may have as many levels as you like. White space (i.e. <spaces> and  <tabs>) are used as delimiters, so you can not have any spaces or tabs in the names of samples, regions, or other identifiers.




HP-Rare runs on the Microsoft Windows operating system that has the .NET platform installed. See my Software page for instructions on how to install this on your computer (it may already be there).

Click  here to download a ZIP file containing HP-Rare and a library of functions (kalinowski_library.dll) that the program needs.


Installation / UnInstallation

To "install," place HP-Rare.exe and kalinowski_library.dll in a folder. Click on HP-Rare to run. Delete both files to "uninstall."




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