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Table of Contents
GENEPOP
Genepop 4.0 (released 2007)
It computes exact tests for Hardy-Weinberg equilibrium, for population
differentiation and for genotypic disequilibrium among pairs of loci;
It computes estimates of F-statistics, null allele frequencies, allele size-
based statistics for microsatellites, etc., and of number of immigrants
by Barton & Slatkin's 1986 private allele method;
It performs analyses of isolation by distance from pairwise comparisons
of individuals or population samples, including con dence intervals for
“neighborhood size”.
Program information
- Windows
- Unix or Linux
- Mac OSX
Data type handled
- haploid/diploid
Input Files
* First line: anything Use this line to store information about your data
- Locus names: They may be given one per line, or on the same line but separated by commas
- Pop sample indicator (Capitalization does not matter): Each sample from a different geographical original is declared by a line with a pop statement
- Information for first individual:
ind#001 fem ,0101 0202 0000 0410
- Here ind#001 fem is an identifier for your personal use. You can use any character (except a comma!).The last identifier of every sub-population is used by Genepop as the sample name in output files. The comma between the identifier and the list of genotypes is required.
- 0101 indicates that this individual is homozygous for the 01 allele at the first locus.
- The same individual is homozygous for the 02 allele at the second locus (0202).
- Unordered List Item Data are missing at the third locus (0000).
- At the fourth locus, the genotype is 0410, which indicates the presence of alleles 04 and 10.
- More individuals: Each individual information starts on a new line, but may extend over several lines (do not start a new line in the middle of a onelocus genotype!)
- More samples: each declared by a pop statement on a new line
- Do not leave blank lines at the end of the file
example:
Title line: "Grape populations in southern France" ADH Locus 1 ADH #2 ADH three ADH-4 ADH-5 mtDNA Pop Grange des Peres , 0201 003003 0102 0302 1011 01 Grange des Peres , 0202 003001 0102 0303 1111 01 Grange des Peres , 0102 004001 0202 0102 1010 01 Grange des Peres , 0103 002002 0101 0202 1011 01 Grange des Peres , 0203 002004 0101 0102 1010 01 POP Tertre Roteboeuf , 0102 002002 0201 0405 0807 01 Tertre Roteboeuf , 0102 002001 0201 0405 0307 01 Tertre Roteboeuf , 0201 002003 0101 0505 0402 01 Tertre Roteboeuf , 0201 003003 0301 0303 0603 01 Tertre Roteboeuf , 0101 002001 0301 0505 0807 01 pop Bonneau 01 , 0101 002002 0304 0805 0304 01 Bonneau 02 , 0201 002002 0404 0505 0304 01 Bonneau 03 , 0101 002100 0304 0505 0101 01 Bonneau 04 , 0101 100100 0204 0805 0304 01 Bonneau 05 , 0101 100002 0104 0808 0304 01 Pop , 0000 002001 0202 0402 0007 01 , 0200 002001 0202 0205 0707 01 , 0010 002001 0101 0105 0807 01 last pop, 0101 002001 0101 0401 0807 02
How to cite
Raymond M. & Rousset F, 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity, 86:248-249