GENETIX

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.

• Windows 95
• Windows NT

• diploid
• Microsat
• RFLP
• AFLP
• SNP (numeric)
• Standard

• can import GENEPOP and FSTAT format
• can convert GENETIX files to GENEPOP, FSTAT and Arlequin

• 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

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

• 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).