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fstat [2007/12/12 12:17] – heidifstat [2010/04/27 15:40] (current) – heidi
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   * Windows (95 and above)   * Windows (95 and above)
   * Macintosh with PC emulation software   * Macintosh with PC emulation software
 +
  
 ===== Data type handled ===== ===== Data type handled =====
   * Microsatellites   * Microsatellites
-  * multi-allelic markers+  * Standard (multi-allelic markers) 
 + 
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 ===== Input Files ===== ===== 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   * named FILENAME.DAT
   * total number of individuals in the data set needs to be less than 20’000     * total number of individuals in the data set needs to be less than 20’000  
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     * Samples need not to be ordered     * 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)     * 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: <code> 
 +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> 
 +  * code for alleles is a two digit number: <code> 
 +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 
 +</code> 
 + 
 +\\ 
 +=== 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: <code> 
 +Stade de France 
 +Twickenham 
 +Arms Park 
 +</code> 
 + 
 +=== multiple regression and partial mantel file: === 
 +No specific extension is required for this file 
 +  * example: <code> 
 +       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  
 +</code> 
  
  
 ===== How to cite ===== ===== How to cite =====
-Goudet, J. 2001. FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3)+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)
fstat.1197458233.txt.gz · Last modified: 2008/07/22 13:30 (external edit)