====== FSTAT ====== **[[http://www2.unil.ch/popgen/softwares/fstat.htm|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) ===== Program information ===== * Windows (95 and above) * Macintosh with PC emulation software ===== Data type handled ===== * Microsatellites * Standard (multi-allelic markers) ===== Input Files ===== input file of format [[GENEPOP]] can be translated to a FSTAT input file in the file conversion menu === FSTAT format: === * 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) \\ === examples: === * code for alleles is a one digit number: 3 5 4 1 loc-1 loc-2 loc-3 loc-4 loc-5 1 44 43 43 33 44 1 44 44 43 33 44 1 44 44 43 43 44 2 44 44 33 32 44 2 44 33 44 43 44 2 44 43 44 43 44 3 44 44 44 43 44 3 44 44 44 44 44 3 44 44 43 21 44 * code for alleles is a two digit number: 3 5 4 2 loc-1 loc-2 loc-3 loc-4 loc-5 1 0404 0403 0403 0303 0404 1 0404 0404 0403 0303 0404 1 0404 0404 0403 0403 0404 2 0404 0404 0303 0302 0404 2 0404 0303 0404 0403 0404 2 0404 0403 0404 0403 0404 3 0404 0404 0404 0403 0404 3 0404 0404 0404 0404 0404 3 0404 0404 0403 0201 0404 \\ === additional label file: === text file containing names (labels) for the population samples: * extension: .LAB * Each line should contain the name (label) of one sample * samples should appear in the same order as in the .DAT file * labels can be any length but will be truncated to six characters in the output files * example: Stade de France Twickenham Arms Park === multiple regression and partial mantel file: === No specific extension is required for this file * example: 8 3 var0 (YANOM.GEN) var1 (YANOM.ANT) var2 (YANOM.GEO) 35.00000 96.00000 9.00000 44.00000 147.00000 28.00000 38.00000 88.00000 20.00000 47.00000 295.00000 152.00000 56.00000 318.00000 161.00000 59.00000 309.00000 178.00000 52.00000 284.00000 149.00000 65.00000 339.00000 158.00000 ===== How to cite ===== Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Available from http://www2.unil.ch/popgen/softwares/fstat.htm. Updated from Goudet (1995)