By browsing our site you accept the installation and use cookies on your computer. Know more

Menu Logo Principal logo partenaire Logo Biogeco

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

Unité mixte de recherche (Inra, Univ. Bordeaux 1)Biodiversité, gènes et communautés (Biogeco) INRA_rvb150Bordeaux1

INRA Bordeaux-Aquitaine

Site de Recherches Forêt-Bois

69 route d'Arcachon

33612 CESTAS Cedex - FRANCE

AFLPdiv

This program is based on the paper by Coart et al. (Conservation Genetics 6:259-273, 2005) and has been written by Rémy Petit (petit_at_pierroton.inra.fr).

README

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]

PLP 5%

PLP 1%

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

VERSIONS

*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

For theoretical help : petit_at_pierroton.inra.fr
For technical help : Frederic.Raspail_at_pierroton.inra.fr

c) Rémy Petit (Petit_at_pierroton.inra.fr), INRA-Bordeaux

Downloads