Differences

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--- geneland [2011/05/20 11:26] – heidi
+++ geneland [2011/05/31 11:38] (current) – heidi
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 ===== Program information =====
 The program is released as an add-on to the free statistical program R and is currently available for Linux, Mac-OS and Windows. It includes a fully clickable user interface requiring no particular knowledge of R.
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 ===== Input Files =====
-==== example: ====
+  * Genotypes file: contains the genotypes of n haploid or diploid individuals at L co-dominant markers
+  * Coordinates file (optional): contains the spatial coordinates representative of each individual.
+\\
+==== Genotypes file ====
+Assuming that you have data for n individuals genotyped at L loci, the data must be arranged in
+  * a plain ascii file
+  * without any extra invisible characters (like in MS-Word .doc files)
+  * with one line per individual
+  * each allele must be coded by an integer
+  * the number of digits of each field is arbitrary and can vary across loci
+  * extra header lines are not allowed
+  * missing data are allowed and can be coded by any arbitrary character string, (e.g. 000, 00, NA or -999). By default, it is assumed that missing data are coded as NA.
+  * for haploid organisms with L loci, the genotype file must have L columns.
+=== diploid data: ===
+  * Codominant data (SNP or Microsat):
+    * one line and 2x L columns per individual
+    * Example (2 individuals with 10 loci, missing data are coded as 000):
 <code>
+000 358 362 141 141 179 000 208 224 243 243 278 284 86 88 120 124 238 244
+202 000 358 141 141 183 183 218 224 237 243 276 278 88 88 120 124 240 244
 </code>
+  * Dominant data (AFLP):
+    * one line and L columns per individual
+    * absence/presence of the allele is coded as 0/1
+    * Example (2 individuals with 10 loci, missing data are coded as 000):
+<code>
+1 1 1 0 1 0 0 0
+0 0 1 1 0 0 1 000
+</code>
+=== haploid data: ===
+  * for Microsat, SNP or mtDNA data
+  * one line and L columns per individual
+  * Example (2 individuals with 10 loci, missing data are coded as 000):
+<code>
+000 358 362 141 141 179 000 208 224
+202 000 358 141 141 183 183 218 224
+</code>
+\\
+==== Coordinates file ====
+  * one line per individual and two columns (x-axis and y-axis coordinate)
+  * the units do not matter
+  * coordinates are planar coordinates such as UTM coordinates. Coordinates given as spherical coordinates will be interpreted as planar coordinates.
+  * extra header lines are not allowed
+  * missing data are not allowed. If some coordinates are missing, you can either substitute an estimated value or do the analysis without spatial coordinates at all using the non spatial model.
+  * Example (2 individuals):
+<code>
+.6 745.2
+.1 827.8
+</code>
+\\