genepop
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====== GENEPOP ====== | ====== GENEPOP ====== | ||
- | **[[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 | + | * **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 |
- | by commas | + | < |
- | * **Pop sample indicator** (Capitalization does not matter): Each sample from a different | + | Title line: "Grape populations in southern France" |
- | geographical original is declared by a line with a pop statement | + | Loc1,Loc2, ADH3, |
+ | Pop | ||
+ | Grange des Peres , 0201 003003 0102 0302 1011 01 | ||
+ | ... | ||
+ | </ | ||
+ | * **Pop sample indicator** (Capitalization does not matter): Each sample from a different geographical original is declared by a line with a pop statement | ||
* **Information for first individual: | * **Information for first individual: | ||
* Here ind#001 fem is an identifier for your personal use. You can use any character (except a comma!).The last identifier of every sub-population is used by Genepop as the sample name in output files. The comma between the identifier and the list of genotypes is required. | * Here ind#001 fem is an identifier for your personal use. You can use any character (except a comma!).The last identifier of every sub-population is used by Genepop as the sample name in output files. The comma between the identifier and the list of genotypes is required. | ||
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* Unordered List Item Data are missing at the third locus (0000). | * Unordered List Item Data are missing at the third locus (0000). | ||
* At the fourth locus, the genotype is 0410, which indicates the presence of alleles 04 and 10. | * At the fourth locus, the genotype is 0410, which indicates the presence of alleles 04 and 10. | ||
- | * **More individuals**: | + | * **More individuals**: |
- | extend over several lines (do not start a new line in the middle of a onelocus | + | |
- | genotype!) | + | |
* **More samples:** each declared by a pop statement on a new line | * **More samples:** each declared by a pop statement on a new line | ||
* Do not leave blank lines at the end of the file | * Do not leave blank lines at the end of the file | ||
\\ | \\ | ||
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==== example: ==== | ==== example: ==== | ||
< | < | ||
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last pop, 0101 002001 0101 0401 0807 02 | last pop, 0101 002001 0101 0401 0807 02 | ||
</ | </ | ||
+ | This example shows some useful features: | ||
+ | * There is no constraint on the number of blanks separating the various fields | ||
+ | * The individual identifer has a free format | ||
+ | * 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 | ||
+ | * haploid and diploid data can be intermixed. (6-digits genotypes are recognized as 3-digits diploid genotypes; 4-digits genotypes are recognized as 2-digits diploid genotypes; 2- and 3-digits genotypes are recognized as haploid genotypes. The same coding should be used consistently within each locus (for haplo-diploid data haploid data should be coded as diploid data with one unknown allele).) | ||
+ | * Genotypes can extend on more than one line | ||
+ | * To group various samples, just remove each relevant Pop separator | ||
+ | |||
+ | ==== 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 to the number of genotypes in each individual | ||
+ | * No empty line should be present in the data file | ||
+ | * accepts input file names either with the extension .txt or without any 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.1196779144.txt.gz · Last modified: 2008/07/22 13:30 (external edit)