Differences

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

--- genepop [2007/12/04 15:39] – heidi
+++ genepop [2011/07/07 11:29] (current) – heidi
@@ Line 1: / Line 1: @@
 ====== GENEPOP ======
-**[[http://genepop.curtin.edu.au/index.html|GENEPOP]]**\\
+**[[http://genepop.curtin.edu.au/genepop_op1.html|GENEPOP]]**\\
+[[http://kimura.univ-montp2.fr/~rousset/Genepop.pdf|documentation]]\\
 [[http://genepop.curtin.edu.au/help_input.html|GENEPOP input file]]
 \\
-Genepop 4.0 (released 2007)\\
+Genepop 4.1 (24.03.2011)\\
-It computes exact tests for Hardy-Weinberg equilibrium, for population
+It computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci;\\
-differentiation and for genotypic disequilibrium among pairs of loci;\\
+It computes estimates of F-statistics, null allele frequencies, allele sizebased statistics for microsatellites, etc., and of number of immigrants by Barton & Slatkin's 1986 private allele method;\\
-It computes estimates of F-statistics, null allele frequencies, allele size-
+It performs analyses of isolation by distance from pairwise comparisons of individuals or population samples, including confidence intervals for "neighborhood size";\\
-based statistics for microsatellites, etc., and of number of immigrants
+Mantel test
-by Barton & Slatkin's 1986 private allele method;\\
-It performs analyses of isolation by distance from pairwise comparisons
-of individuals or population samples, including con dence intervals for
-"neighborhood size".
 ===== Program information =====
   * Windows
-  * Unix or Linux
+  * Linux
   * Mac OSX
 ===== Data type handled =====
   * haploid/diploid
+  * Microsattelite
+  * Standard (multi-allelic markers)
 ===== Input Files =====
-* **First line:** anything Use this line to store information about your data
+  * **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
+<code>
-  * **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,ADH4,ADH5,mtDNA
+Pop
+Grange des Peres , 0201 003003 0102 0302 1011 01
+...
+</code>
+  * **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:** <code>ind#001 fem ,0101 0202 0000 0410</code>
     * 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.
@@ Line 34: / Line 42: @@
     * 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.
-  * **More individuals**: Each individual information starts on a new line, but may
+  * **More individuals**: Each individual information starts on a new line, but may extend over several lines (do not start a new line in the middle of a onelocus genotype!)
-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
   * Do not leave blank lines at the end of the file
 \\
 ==== example: ====
 <code>
@@ Line 75: / Line 86: @@
 last pop, 0101 002001 0101 0401 0807 02
 </code>
+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
 ===== How to cite =====
-Raymond M. & Rousset F, 1995. GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J. Heredity, 86:248-249
+Rousset F, 2008. GENEPOP'007: a complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 1:103-106