Table of Contents
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(c) Rémy Petit (Petit@pierroton.inra.fr), INRA-Bordeaux
This program is based on the paper by Coart et al. (Conservation Genetics 6:259-273, 2005)
and has been written by Rémy J. Petit (Petit@pierroton.inra.fr).
It computes comparable measures of diversity (allelic richness and % polymorphic loci) from AFLP data.
The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the
following information:
First line : Number of AFLP loci (=polymorphic band) Number of populations Rarefaction sample size (equal or lower than the smallest
population sample size)
Second line: Population sample sizes
Subsequent lines:
Locus 1: Number of [+] genotypes in pop 1, 2...
Locus 2: Number of [+] genotypes in pop 1, 2...
...
See the example (aflptest.txt and aflptest.out)
No column should be empty and each population (row) should be composed of AT LEAST 3 individuals.
Good luck!
ex:
aflptest.txt
6 3 10
60 100 100
5 100 98
9 47 50
8 35 29
5 100 98
9 47 50
8 35 2
aflptest.out
RESULTS OF THE ANALYSIS OF DIVERSITY
Nb loci= 6 Nb Pop= 3
Results per population
Rarefaction to: 10
Pop Eff_Pop Pb[ 10] PLP5% PLP1% Mrk 1 Mrk 2 Mrk 3 Mrk 4 Mrk 5 Mrk 6
1 60 1.744 1.000 1.000 1.612 1.831 1.790 1.612 1.831 1.790
2 100 1.663 0.000 0.333 1.000 1.999 1.990 1.000 1.999 1.990
3 100 1.591 0.500 0.667 1.191 1.999 1.973 1.191 1.999 1.191
2 VERSIONS:
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*Version 1.1 (05/2007):
Fix the bug on the computation of PLP1% and PLP5% (found by Inga MICHALCZYK Philipps-Universität Marburg)
*Version 1.0 (10/2005) :
No Parameters Limitation:
the number of diallelic loci is not limited to 160
the number of populations is not limited to 20
New Graphical Interface.
Delphi Program.
*First Version;
Parameters limitation size:
the number of diallelic loci limited to 160
the number of populations limited to 20
Turbo Pascal Program
HELP
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For theoretical help: Remy.Petit@pierroton.inra.fr
For technical help: Frederic.Raspail@pierroton.inra.fr