arlequin
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- | **[[http://cmpg.unibe.ch/ | + | **[[http://popgen.unibe.ch/ |
+ | [[http:// | ||
\\ | \\ | ||
- | 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 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; | ||
===== Program information ===== | ===== Program information ===== | ||
* program written in C++ | * program written in C++ | ||
- | * Windows version (2000, XP, and above) | + | * Windows version (XP, Vista, 7) |
+ | * LINUX | ||
\\ | \\ | ||
+ | |||
===== Data type handled ===== | ===== Data type handled ===== | ||
* DNA sequences | * DNA sequences | ||
* RFLP | * RFLP | ||
+ | * SNP | ||
* Microsattelite | * Microsattelite | ||
* Standard data | * Standard data | ||
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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: ==== | ||
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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} | } | ||
</ | </ | ||
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==== Profile section: ==== | ==== Profile section: ==== | ||
- | * Title (string within “”): | + | * Title (string within “”): |
- | * Number of samples (int 1-1000): | + | * Number of samples (int 1-1000): |
- | * Type of data (DNA, RFLP, MICROSAT, STANDARD, FREQUENCY): | + | * Type of data (DNA, RFLP, MICROSAT, STANDARD, FREQUENCY): |
- | * Haplotypic/ | + | * Haplotypic/ |
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* Optionally (__default value__): | * Optionally (__default value__): | ||
- | * locus separator (__WHITESPACE__, | + | * locus separator (__WHITESPACE__, |
- | * gametic phase known/ | + | * gametic phase known/ |
- | * recessive/ co-dominant allele (1/ | + | * recessive/ co-dominant allele (1/ |
- | * code for recessive allele (string within __“null”__): | + | * code for recessive allele (string within __“null”__): |
- | * code for missing data (character within __“?”__ or __‘? | + | * code for missing data (character within __“?”__ or __‘? |
- | * frequencies as absolute/ | + | * frequencies as absolute/ |
- | * 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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=== Samples (obligatory): | === Samples (obligatory): | ||
Defines haplotypic/ | Defines haplotypic/ | ||
- | * name for each sample (string within “”): | + | * name for each sample (string within “”): |
- | * size of sample (int value): | + | * size of sample (int value): |
* data itself (list of haplotypes or genotypes and their frequencies, | * data itself (list of haplotypes or genotypes and their frequencies, | ||
< | < | ||
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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): |
* group definitions (list containing the names of the samples belonging to the group, entered within braces): | * group definitions (list containing the names of the samples belonging to the group, entered within braces): | ||
< | < | ||
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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/ | + | * number of matrices among which we compute the correlations (2/ |
- | * matrix that is used as genetic distance (" | + | * matrix that is used as genetic distance (" |
* labels that identify the columns of the YMatrix (list containing the names of the lable name belonging to the group, entered within braces): | * labels that identify the columns of the YMatrix (list containing the names of the lable name belonging to the group, entered within braces): | ||
< | < | ||
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} | } | ||
</ | </ | ||
+ | |||
+ | |||
+ | ===== How to cite ===== | ||
+ | Excoffier, L. and H.E. L. Lischer (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources. 10: 564-567. | ||
arlequin.1196696113.txt.gz · Last modified: 2008/07/22 13:30 (external edit)