fstat
Differences
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fstat [2007/12/12 12:22] – heidi | fstat [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 | ||
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===== 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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* 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) | ||
- | === example: === | + | \\ |
- | < | + | === examples: === |
- | 6 | + | * code for alleles is a one digit number: |
+ | 3 | ||
loc-1 | loc-1 | ||
loc-2 | loc-2 | ||
Line 48: | Line 64: | ||
loc-4 | loc-4 | ||
loc-5 | loc-5 | ||
- | + | 1 44 43 43 33 44 | |
- | 1 44 43 43 33 44 | + | |
- | 1 | + | |
- | 1 44 44 43 43 44 | + | |
- | 1 44 44 0 33 44 | + | |
- | 1 | + | |
- | 1 44 44 0 43 44 | + | |
- | 1 44 44 43 43 44 | + | |
- | 1 | + | |
- | 2 44 44 33 32 44 | + | |
- | 2 44 33 44 43 44 | + | |
- | 2 | + | |
- | 2 44 44 33 33 44 | + | |
- | 2 44 43 44 44 44 | + | |
- | 2 44 44 44 22 44 | + | |
- | 2 | + | |
- | 2 | + | |
- | 3 44 44 44 43 44 | + | |
- | 3 44 44 44 44 44 | + | |
- | 3 | + | |
- | 3 44 44 33 43 44 | + | |
- | 3 44 44 43 21 44 | + | |
- | 4 44 44 43 44 44 | + | |
- | 4 44 44 43 43 44 | + | |
- | 4 44 44 43 43 44 | + | |
- | 4 44 44 43 44 44 | + | |
- | 4 44 44 43 44 44 | + | |
- | 4 44 44 44 33 44 | + | |
- | 4 44 44 44 44 44 | + | |
- | 5 44 44 44 21 44 | + | |
- | 5 44 44 44 33 44 | + | |
- | 5 44 44 43 43 44 | + | |
- | 5 44 44 43 43 44 | + | |
- | 5 44 44 44 44 44 | + | |
- | 5 44 44 44 43 44 | + | |
- | 5 44 44 43 43 44 | + | |
- | 5 44 44 44 0 44 | + | |
- | 5 44 43 44 43 44 | + | |
- | 6 44 44 44 43 44 | + | |
- | 6 44 44 43 33 44 | + | |
- | 6 44 44 44 32 44 | + | |
- | 6 44 44 43 41 44 | + | |
- | 6 44 44 44 44 44 | + | |
- | 6 44 44 44 42 44 | + | |
- | 6 44 44 44 43 44 | + | |
</ | </ | ||
- | < | + | * code for alleles is a two digit number: |
- | 6 | + | 3 |
loc-1 | loc-1 | ||
loc-2 | loc-2 | ||
Line 104: | Line 84: | ||
1 0404 0404 0403 0303 0404 | 1 0404 0404 0403 0303 0404 | ||
1 0404 0404 0403 0403 0404 | 1 0404 0404 0403 0403 0404 | ||
- | 1 0404 0404 0 0303 0404 | ||
- | 1 0404 0404 0204 0304 0404 | ||
- | 1 0404 0404 0 0403 0404 | ||
- | 1 0404 0404 0403 0403 0404 | ||
- | 1 0404 0404 0 0403 0404 | ||
2 0404 0404 0303 0302 0404 | 2 0404 0404 0303 0302 0404 | ||
2 0404 0303 0404 0403 0404 | 2 0404 0303 0404 0403 0404 | ||
2 0404 0403 0404 0403 0404 | 2 0404 0403 0404 0403 0404 | ||
- | 2 0404 0404 0303 0303 0404 | ||
- | 2 0404 0403 0404 0404 0404 | ||
- | 2 0404 0404 0404 0202 0404 | ||
- | 2 0404 0404 0403 0403 0404 | ||
- | 2 0404 0404 0404 0404 0404 | ||
3 0404 0404 0404 0403 0404 | 3 0404 0404 0404 0403 0404 | ||
3 0404 0404 0404 0404 0404 | 3 0404 0404 0404 0404 0404 | ||
3 0404 0404 0403 0201 0404 | 3 0404 0404 0403 0201 0404 | ||
- | 3 0404 0404 0303 0403 0404 | ||
- | 3 0404 0404 0403 0201 0404 | ||
- | 4 0404 0404 0403 0404 0404 | ||
- | 4 0404 0404 0403 0403 0404 | ||
- | 4 0404 0404 0403 0403 0404 | ||
- | 4 0404 0404 0403 0404 0404 | ||
- | 4 0404 0404 0403 0404 0404 | ||
- | 4 0404 0404 0404 0303 0404 | ||
- | 4 0404 0404 0404 0404 0404 | ||
- | 5 0404 0404 0404 0201 0404 | ||
- | 5 0404 0404 0404 0303 0404 | ||
- | 5 0404 0404 0403 0403 0404 | ||
- | 5 0404 0404 0403 0403 0404 | ||
- | 5 0404 0404 0404 0404 0404 | ||
- | 5 0404 0404 0404 0403 0404 | ||
- | 5 0404 0404 0403 0403 0404 | ||
- | 5 0404 0404 0404 0 0404 | ||
- | 5 0404 0403 0404 0403 0404 | ||
- | 6 0404 0404 0404 0403 0404 | ||
- | 6 0404 0404 0403 0303 0404 | ||
- | 6 0404 0404 0404 0302 0404 | ||
- | 6 0404 0404 0403 0401 0404 | ||
- | 6 0404 0404 0404 0404 0404 | ||
- | 6 0404 0404 0404 0402 0404 | ||
- | 6 0404 0404 0404 0403 0404 | ||
</ | </ | ||
\\ | \\ | ||
- | * input file of format [[GENEPOP]] or [[FSTAT]] | + | === additional label file: === |
+ | text file containing names (labels) for the population samples: | ||
+ | * extension: .LAB | ||
+ | * Each line should contain the name (label) | ||
+ | * samples should appear in the same order as in the .DAT file | ||
+ | * labels | ||
+ | * example: < | ||
+ | Stade de France | ||
+ | Twickenham | ||
+ | Arms Park | ||
+ | </ | ||
+ | |||
+ | === multiple regression and partial mantel | ||
+ | No specific extension is required for this file | ||
+ | * example: < | ||
+ | | ||
+ | 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 ===== | ===== 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:// |
fstat.1197458569.txt.gz · Last modified: 2008/07/22 13:30 (external edit)