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INRA
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Dernière mise à jour : Mai 2018

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Unité Mixte de Recherche Inra-Univ. Bordeaux 1 "Biodiversité Gènes et Communautés" - Biogeco

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Rarefac

This programme (RAREFAC) is written in Turbo-Pascal and relates to the following paper :

Petit, El Mousadik & Pons. 1998. Identifying populations for conservation on the basis of genetic markers. Conservation Biology12, 844-855. It is a simplified version of the programme CONTRIB providing just the option of rarefaction and the partitioning of allelic richness within and among populations. This is contrasted with equivalent measurements for H, the expected heterozygosity.

It can be used in conjunction with the program haplodiv based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters.

The input file is a text file, where the first line indicates the number of haplotypes (limited to 100), then the number of populations (limited to 50), and finally the rarefaction size (it should not be larger than the smallest population sample size.

Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies). Example:

 18 4 10
 1 0 1 0 0 0 1 1 ...(18 columns)
 0 1 2 1 1 0 13 0 ...
 0 0 8 0 0 3 6 0 ...
 1 0 9 0 0 3 7 1

Results can be seen in the output file. General measures are given first: Within population diversity (HS), total diversity (HT), and GST are given, followed by similar measures based on allelic richness. Then you get the results for each population: H, its standard error, and allelic richness after rarefaction (minus one: a monomorphic population has one allele which has to be removed to compute the partitioning of diversity within and among populations).

The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or Rst. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. Then compute the ratio of the two means.!

(c) Rémy Petit (petit_at_pierroton.inra.fr), INRA-Bordeaux, April 2003.

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