Differences

This shows you the differences between two versions of the page.

--- fstat [2007/12/12 11:52] – heidi
+++ fstat [2010/04/27 15:40] (current) – heidi
@@ Line 9: / Line 9: @@
   * Windows (95 and above)
   * Macintosh with PC emulation software
 ===== Data type handled =====
   * Microsatellites
-  * multi-allelic markers
+  * 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: <code>
+  5  4  1
+loc-1
+loc-2
+loc-3
+loc-4
+loc-5
+   44 43 43 33 44
+   44 44 43 33 44
+   44 44 43 43 44
+   44 44 33 32 44
+   44 33 44 43 44
+   44 43 44 43 44
+   44 44 44 43 44
+   44 44 44 44 44
+   44 44 43 21 44
+</code>
+  * code for alleles is a two digit number: <code>
+  5  4  2
+loc-1
+loc-2
+loc-3
+loc-4
+loc-5
+       0404 0403 0403 0303 0404
+       0404 0404 0403 0303 0404
+       0404 0404 0403 0403 0404
+       0404 0404 0303 0302 0404
+       0404 0303 0404 0403 0404
+       0404 0403 0404 0403 0404
+       0404 0404 0404 0403 0404
+       0404 0404 0404 0404 0404
+       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>
+	     3
+var0 (YANOM.GEN)
+var1 (YANOM.ANT)
+var2 (YANOM.GEO)
+.00000	96.00000	 9.00000
+.00000	147.00000	28.00000
+.00000	88.00000	20.00000
+.00000	295.00000	152.00000
+.00000	318.00000	161.00000
+.00000	309.00000	178.00000
+.00000	284.00000	149.00000
+.00000	339.00000	158.00000
+</code>
 ===== 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)