structure
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structure [2007/12/07 10:08] – heidi | structure [2011/07/07 12:54] – heidi | ||
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====== STRUCTURE ====== | ====== STRUCTURE ====== | ||
- | {{structure.jpg? | + | {{structure.jpg? |
\\ | \\ | ||
- | **[[http:// | + | **[[http:// |
[[http:// | [[http:// | ||
\\ | \\ | ||
- | Version 2.2 (April | + | Version 2.3.3 (January 2010)\\ |
- | The program structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers. | + | The program structure implements a model-based clustering method for inferring population structure using genotype data consisting of unlinked markers. |
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* Windows | * Windows | ||
* Mac OS X | * Mac OS X | ||
+ | |||
===== Data type handled ===== | ===== Data type handled ===== | ||
- | * SNP | + | * SNP (numeric) |
* Microsatellites | * Microsatellites | ||
* RFLP | * RFLP | ||
* AFLP | * AFLP | ||
*dipoid/ | *dipoid/ | ||
+ | |||
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The entire data set is arranged as a matrix in a single file, in which the data for individuals are in rows, and the loci are in columns. For a diploid organism, data for each individual can be stored either as 2 consecutive rows, where each locus is in one column, or in one row, where each locus is in two consecutive columns. | The entire data set is arranged as a matrix in a single file, in which the data for individuals are in rows, and the loci are in columns. For a diploid organism, data for each individual can be stored either as 2 consecutive rows, where each locus is in one column, or in one row, where each locus is in two consecutive columns. | ||
- | \\ | ||
=== rows: === | === rows: === | ||
* **Marker Names** (Optional; string): | * **Marker Names** (Optional; string): | ||
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one or more rows. | one or more rows. | ||
- | \\ | ||
=== Individual/ | === Individual/ | ||
Each row of individual data contains the following elements. These form columns in the data file: | Each row of individual data contains the following elements. These form columns in the data file: | ||
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* **Genotype Data** (Required; integer): Each allele at a given locus should be coded by a unique integer (eg microsatellite repeat score). | * **Genotype Data** (Required; integer): Each allele at a given locus should be coded by a unique integer (eg microsatellite repeat score). | ||
- | \\ | ||
=== Missing genotype data: === | === Missing genotype data: === | ||
Missing data should be indicated by a number that doesn' | Missing data should be indicated by a number that doesn' | ||
\\ | \\ | ||
+ | |||
==== example: ==== | ==== example: ==== | ||
- | example for the genotype data: | + | example for genotype data: |
< | < | ||
loc_a loc_b loc_c loc_d loc_e | loc_a loc_b loc_c loc_d loc_e | ||
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Carsten | Carsten | ||
</ | </ | ||
+ | |||
===== How to cite ===== | ===== How to cite ===== | ||
The basic algorithm :\\ | The basic algorithm :\\ | ||
- | Pritchard, J. K., Stephens, M., and Donnelly, P. (2000a). Inference of population structure using | + | * Pritchard, J. K., Stephens, M., and Donnelly, P. (2000a). Inference of population structure using multilocus genotype data. Genetics, 155:945-959. |
- | multilocus genotype data. Genetics, 155:945{959. | + | |
\\ | \\ | ||
Extensions to the method:\\ | Extensions to the method:\\ | ||
- | Falush, D., Stephens, M., and Pritchard, J. K. (2003a). Inference of population structure: | + | * Falush, D., Stephens, M., and Pritchard, J. K. (2003a). Inference of population structure: |
- | sions to linked loci and correlated allele frequencies. Genetics, 164:1567{1587.\\ | + | |
- | and\\ | + | * Hubisz M. J., et al. (2009). Inferring weak population structure with the assistance of |
- | Falush, D., Stephens, M., and Pritchard, J. K. (2007). Inference of population structure using | + | sample group information. Molecular Ecology Resources, 9:1322-32. |
- | multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes. | + |
structure.txt · Last modified: 2011/07/07 12:54 by heidi