geneland
Differences
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| ===== Input Files ===== | ===== Input Files ===== | ||
| * Genotypes file: contains the genotypes of n haploid or diploid individuals at L co-dominant markers | * Genotypes file: contains the genotypes of n haploid or diploid individuals at L co-dominant markers | ||
| - | * Geographic information | + | * Coordinates |
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| ==== Genotypes file ==== | ==== Genotypes file ==== | ||
| Assuming that you have data for n individuals genotyped at L loci, the data must be arranged in | Assuming that you have data for n individuals genotyped at L loci, the data must be arranged in | ||
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| * for haploid organisms with L loci, the genotype file must have L columns. | * for haploid organisms with L loci, the genotype file must have L columns. | ||
| - | === diploid data === | + | === diploid data: === |
| - | Codominant data (SNP or Microsat): | + | |
| - | * one line and 2x L columns per individual | + | * one line and 2x L columns per individual |
| - | * Example (2 individuals with 10 loci, missing data are coded as 000): | + | * Example (2 individuals with 10 loci, missing data are coded as 000): |
| < | < | ||
| 198 000 358 362 141 141 179 000 208 224 243 243 278 284 86 88 120 124 238 244 | 198 000 358 362 141 141 179 000 208 224 243 243 278 284 86 88 120 124 238 244 | ||
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| </ | </ | ||
| - | ==== example: ==== | + | * Dominant data (AFLP): |
| + | * one line and L columns per individual | ||
| + | * absence/ | ||
| + | * Example (2 individuals with 10 loci, missing data are coded as 000): | ||
| < | < | ||
| + | 0 1 1 1 0 1 0 0 0 | ||
| + | 1 0 0 1 1 0 0 1 000 | ||
| </ | </ | ||
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| + | === 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): | ||
| + | < | ||
| + | 198 000 358 362 141 141 179 000 208 224 | ||
| + | 200 202 000 358 141 141 183 183 218 224 | ||
| + | </ | ||
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| + | \\ | ||
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| + | ==== 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): | ||
| + | < | ||
| + | 25.6 745.2 | ||
| + | 54.1 827.8 | ||
| + | </ | ||
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| + | \\ | ||
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geneland.1305884329.txt.gz · Last modified: 2011/05/20 11:38 by heidi