FSTAT

version 2.9.3.2 (Feb. 2002)
FSTAT estimates and tests gene diversities and differentiation statistics from codominant genetic markers. It computes both Nei and Weir & Cockerham families of estimators of gene diversities and F-statistics, and tests them using randomisation methods. Jackknife and Bootstrap confidence intervals are also provided. The windows version also estimates statistics developed for the stepwise mutation model (Rst and the like)

• Windows (95 and above)
• Macintosh with PC emulation software

• Microsatellites
• multi-allelic markers

• named FILENAME.DAT
• total number of individuals in the data set needs to be less than 20’000
• first line: contains 4 numbers separated by any number of spaces:
  • number of samples, np (‹=200)
  • number of loci, nl (‹=100)
  • highest number used to label an allele, nu (‹=999)
  • a 1 if the code for alleles is a one digit number (1-9), a 2 if code for alleles is a 2 digit number (01-99) or a 3 if code for alleles is a 3 digit number (001-999)
• followed by nl lines:
  • each containing the name of a locus, in the order they will appear in the rest of the file
  • On line nl+2, a series of numbers as follow: 1 0102 0103 0101 0203 0 0303
    • first number: identifies the sample to which the individual belongs
    • second: the genotype of the individual at the first locus, coded with a 2 digits number for each allele
    • third: the genotype at the second locus, until locus nl is entered (in the example above, nl=6)
  • Missing genotypes are encoded with 0 (0001 or 0100 are not a valid format, so both alleles at a locus have to be known, otherwise, the genotype is considered as missing)
  • no empty lines are needed between samples
  • number of spaces between genotypes can be anything
  • Numbering of samples need not be sequential
  • the number of samples np needs to be the same as the largest sample identifier
  • Samples need not to be ordered
  • nu needs to be equal to the largest code given to an allele (even if there are less than nu alleles)

Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3)