arlequin
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arlequin [2007/12/07 11:41] – heidi | arlequin [2011/07/07 11:16] (current) – heidi | ||
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- | **[[http://cmpg.unibe.ch/ | + | **[[http://popgen.unibe.ch/ |
- | [[http://cmpg.unibe.ch/ | + | [[http://popgen.unibe.ch/ |
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- | Arlequin ver 3.11 (released | + | Arlequin ver 3.5 (released |
The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples.\\ | The goal of Arlequin is to provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples.\\ | ||
The analyses Arlequin can perform on the data fall into two main categories: intra-population and inter-population methods.\\ | The analyses Arlequin can perform on the data fall into two main categories: intra-population and inter-population methods.\\ | ||
Computes indices of genetic diversity, F-statistics and genetic distances between populations; | Computes indices of genetic diversity, F-statistics and genetic distances between populations; | ||
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===== Program information ===== | ===== Program information ===== | ||
* program written in C++ | * program written in C++ | ||
- | * Windows version (2000, XP, and above) | + | * Windows version (XP, Vista, 7) |
+ | * LINUX | ||
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===== Input Files ===== | ===== Input Files ===== | ||
- | Contain the description of the properties of the data, as well as the raw data themselves. | + | Contain the description of the properties of the data, as well as the raw data themselves. The input files should have a " |
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==== example: ==== | ==== example: ==== | ||
The following small example is a project file containing four populations. The data type is STANDARD genotypic data with unknown gametic phase: | The following small example is a project file containing four populations. The data type is STANDARD genotypic data with unknown gametic phase: | ||
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* significant digits for haplotype frequency outputs (real number 1e-2 – 1e-7(__1e-5__)): | * significant digits for haplotype frequency outputs (real number 1e-2 – 1e-7(__1e-5__)): | ||
* convergence criterion for the EM algorithm (real number __1e-7__ – 1e-12): '' | * convergence criterion for the EM algorithm (real number __1e-7__ – 1e-12): '' | ||
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=== Genetic structure (only required for AMOVA): === | === Genetic structure (only required for AMOVA): === | ||
specifies the hierarchical genetic structure of the samples. It is possible to define groups of populations. | specifies the hierarchical genetic structure of the samples. It is possible to define groups of populations. | ||
- | * start of the subsection: | + | * start of the subsection: |
* name for the genetic structure (string within "" | * name for the genetic structure (string within "" | ||
* number of groups defined in the structure (int value): '' | * number of groups defined in the structure (int value): '' | ||
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=== Mantel test settings === | === Mantel test settings === | ||
allows to specify some distance matrices. The goal is to compute a correlation between the Ymatrix and X1 or a partial correlation between the Ymatrix, X1 and X2. The Ymatrix can be either a pairwise population FST matrix or a custom matrix entered into the project by the user. X1 (and X2) have to be defined in the project. | allows to specify some distance matrices. The goal is to compute a correlation between the Ymatrix and X1 or a partial correlation between the Ymatrix, X1 and X2. The Ymatrix can be either a pairwise population FST matrix or a custom matrix entered into the project by the user. X1 (and X2) have to be defined in the project. | ||
- | * start of the subsection: | + | * start of the subsection: |
* size of the matrices (pos. int value): '' | * size of the matrices (pos. int value): '' | ||
* number of matrices among which we compute the correlations (2/3): '' | * number of matrices among which we compute the correlations (2/3): '' | ||
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} | } | ||
</ | </ | ||
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===== How to cite ===== | ===== How to cite ===== | ||
- | Excoffier, L. G. Laval, | + | Excoffier, L. and H.E. L. Lischer |
arlequin.1197024101.txt.gz · Last modified: 2008/07/22 13:30 (external edit)