Geneland
| Geneland | |
|---|---|
| Basic data
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| Maintainer | Gilles Guillot |
| operating system | Windows, Linux, macOS |
| programming language | Fortran, R. |
| http://www2.imm.dtu.dk/~gigu/Geneland/ | |
Geneland is a computer program and was created by Gilles Guillot. Geneland can be called up as an extension in the statistics software R or as a program with its own user interface . Geneland is used to apply statistical models to population genetic data with spatial location. The data are clustered into a certain number of populations (or groups), each population should be as homogeneous as possible. This clustering is not only based on spatial and genetic data, but phenotypic data can also be used.
The program runs on Windows , Unix and MacOS . Most of Geneland was written in Fortran and little knowledge of R is required for the user.
The main function of Geneland is to use georeferenced individual multilocus genotypes to determine the number of populations and the spatial localization of genetic discontinuities between them. These methods can also be applied to data where all values are equally possible and the number of populations is unknown. The distribution of the populations is assumed in the form of polygons , and the Hardy-Weinberg equilibrium is assumed in each population. The models assume unknown allele frequencies in each population, which is why these are declared as random variables ( Dirichlet or Falush).
As output, the user receives plots of the spatial distribution of individuals and the allocation of each individual to a population based on phenotypic, spatial and genetic data. If you combine Geneland with other R packages such as RgoogleMaps, the distribution of individuals and populations can even be displayed on a GoogleMap.
Geneland uses the Markov Chain Monte Carlo method , which is why the calculation is broken down into a long series of simple operations. A run consisting of 100,000 iterations for a data set with 200 individuals and 10 loci can take 3–15 minutes, depending on the model and the capabilities of the computer.
See also
Individual evidence
- ↑ Gilles Guillot, Frédéric Mortier, Arnaud Estoup: Geneland: a computer package for landscape genetics . In: Molecular Ecology Notes . tape 5 , no. 3 , September 1, 2005, ISSN 1471-8286 , p. 712–715 , doi : 10.1111 / j.1471-8286.2005.01031.x ( wiley.com [accessed February 15, 2018]).
- ↑ The geneland development group: Population genetic and morphometric data analysis using R and the Geneland program. (PDF) (No longer available online.) 2017, archived from the original on April 13, 2018 ; accessed on February 15, 2018 . Info: The archive link was inserted automatically and has not yet been checked. Please check the original and archive link according to the instructions and then remove this notice.
