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Table of Contents
GENETIX
Version 4.05 (05.05.2004)
This set of programs computes several basic parameters of population genetics such as Nei's D and H, Wright's F-statistics (the Weir-Cockerham's and Robertson-Hill's estimators), and linkage disequilibrium D according to Black & Krafsur. For each of them, the distribution of the parameter values under the null hypothesis (for instance Hardy-Weinberg equilibrium for Fstats) is generated by the appropriate resampling scheme of the relevant objects (e.g. alleles between individuals in the case of Fis) using permutations. The permutation-based statistical inference procedures implemented in GENETIX represent an alternative to bootstrapping and jack-knifing, or to exact probability tests when available (see GENEPOP; Raymond & Rousset 1995). In addition, an adaptation of Mantel's test for the correlation between distance matrices is available. A correspondence analysis program adapted to individual diploid genotypes, with tridimensional graphics, is also implemented.
Program information
- Windows 95
- Windows NT
Data type handled
- diploid
- Microsat
- RFLP
- AFLP
- SNP (numeric)
- Standard
Input Files
- file extension: .gtx
- ASCII file
- text separator: blancs, tabulators or other
- 1. line: number of locus
- 2. line: number of populations
- 3. line: name of first locus, maximal 5 characters
- 4. line: number of alleles followed by a list of alleles coded with 3 numbers
- 5. line: name of second locus
- …
- n. line: name of the first population (only 15 characters are taken)
- n+1. line: number of samples
- n+2. line: identifier of the individual of 10 characters length followed by his genotype (locus have the same order as in the list above (6 numbers per locus)
- …
- m. line: name of the second population
- …
- genotype coding:
- 6 numbers
- first allele: first 3 numbers
- second allele: last 3 numbers
- the smaller allele have to come first!
- missing values:
- coded as 000000
- if one allele is unknown then the whole genotype is coded as missing
- haploids:
- coded as homozygous diploids
example
4 2 aat1 1 120 aat2 3 100 132 146 adh 2 100 123 est1 4 100 107 110 115 Population "i" 3 i001 120120 132132 100100 107110 i002 120120 132132 100100 107110 i003 120120 100132 100100 110110 Population "j" 5 j001 120120 132132 100100 107107 j002 120120 132132 100123 107107 j003 120120 100132 100100 107107 j004 120120 100100 100123 000000 j005 120120 100132 100123 107110
How to cite
- Belkhir K., Borsa P., Chikhi L., Raufaste N. & Bonhomme F. 1996-2004 GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, CNRS UMR 5171, Université de Montpellier II, Montpellier (France).