====== FSTAT ======
**[[http://www2.unil.ch/popgen/softwares/fstat.htm|FSTAT]]**
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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)
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=== 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
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=== 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)