genepop
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====== GENEPOP ====== | ====== GENEPOP ====== | ||
- | **[[http:// | + | **[[http:// |
[[http:// | [[http:// | ||
[[http:// | [[http:// | ||
\\ | \\ | ||
- | Genepop 4.0 (released 2007)\\ | + | Genepop 4.1 (24.03.2011)\\ |
- | It computes exact tests for Hardy-Weinberg equilibrium, | + | It computes exact tests for Hardy-Weinberg equilibrium, |
- | differentiation and for genotypic disequilibrium among pairs of loci;\\ | + | It computes estimates of F-statistics, |
- | It computes estimates of F-statistics, | + | It performs analyses of isolation by distance from pairwise comparisons of individuals or population samples, including |
- | based statistics for microsatellites, | + | Mantel test |
- | by Barton & Slatkin' | + | |
- | It performs analyses of isolation by distance from pairwise comparisons | + | |
- | of individuals or population samples, including | + | |
- | " | + | |
===== Program information ===== | ===== Program information ===== | ||
* Windows | * Windows | ||
- | * Unix or Linux | + | * Linux |
* Mac OSX | * Mac OSX | ||
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===== Data type handled ===== | ===== Data type handled ===== | ||
* haploid/ | * haploid/ | ||
+ | * Microsattelite | ||
+ | * Standard (multi-allelic markers) | ||
| | ||
===== Input Files ===== | ===== Input Files ===== | ||
- | * **First line:** anything Use this line to store information about your data | + | |
* **Locus names:** They may be given one per line, or on the same line but separated by commas. This could be useful to clearly label each column | * **Locus names:** They may be given one per line, or on the same line but separated by commas. This could be useful to clearly label each column | ||
< | < | ||
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This example shows some useful features: | This example shows some useful features: | ||
* There is no constraint on the number of blanks separating the various fields | * There is no constraint on the number of blanks separating the various fields | ||
- | * The individual | + | * The individual |
* Alleles are numbered from 01 to 99 or 001 to 999 if needed. 2-digits and 3-digits coding of alleles can be intermixed (among loci, not within loci!) | * Alleles are numbered from 01 to 99 or 001 to 999 if needed. 2-digits and 3-digits coding of alleles can be intermixed (among loci, not within loci!) | ||
* To designate alleles, consecutive numbers are not required | * To designate alleles, consecutive numbers are not required | ||
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* Genotypes can extend on more than one line | * Genotypes can extend on more than one line | ||
* To group various samples, just remove each relevant Pop separator | * To group various samples, just remove each relevant Pop separator | ||
- | \\ | + | |
- | \\ | + | ==== constraints: |
- | There are however constraints | + | * Missing data should be indicated with 00 (or 000 for 3-digits coding) and not with blanks |
+ | * The number of locus names should correspond | ||
+ | * No empty line should | ||
+ | * accepts input file names either with the extension | ||
+ | * input files are ASCII text files | ||
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===== How to cite ===== | ===== How to cite ===== | ||
- | Raymond M. & Rousset F, 1995. GENEPOP | + | Rousset F, 2008. GENEPOP'007: a complete re-implementation of the genepop |
genepop.1196848105.txt.gz · Last modified: 2008/07/22 13:30 (external edit)