Geneland
Geneland
| Geneland | |
|---|---|
| Developer(s) | Gilles Guillot |
| Written in | Fortran, R |
| Operating system | Windows, Linux, MacOS |
| Website | www2.imm.dtu.dk/~gigu/Geneland/ |
Geneland Archived 2018-01-24 at the Wayback Machine is computer software created by Gilles Guillot used as a package for the free statistical software R or as software with a user-friendly interface. The software computes spatial statistical models on population genetics data. It clusters your data into a certain number of populations (groups) where each population is homogeneous. The clustering is based on phenotypic data, spatial data and genetic data.
The software can be run on Windows, Unix and MacOS. The core of Geneland is written in Fortran and only a little knowledge of R is needed to run it.[1]
The main function of this software is to use georeferenced individual multilocus genotype data to decide the number of populations and the spatial location of genetic discontinuities between decided populations. Methods can be used on data where all values are considered to be equally possible and where we don’t know the number of populations. Populations need to be spread over areas described by polygons in space and the Hardy-Weinberg equilibrium is assumed in each population. Moreover, the model assumes that we don’t know the allele frequencies in each population; therefore, all allele frequencies are treated as random variables by Dirichlet model or Falush model.[2]
As a result, the user can get plots containing spatial distributions of individuals, and maps showing into which population each individual belongs based on phenotypic data, spatial data, and genetic data. Combining Geneland with other R packages, such as RgoogleMaps, the user can get as a result a Google map with the spatial distribution of the populations and individuals.
Geneland uses Markov Chain Monte-Carlo (MCMC) technique; therefore, the computing tasks are composed of a long sequence of simple tasks. A run of 100,000 iterations for a dataset of 200 individuals at 10 loci can take around 3-15 minutes, but the computing time depends on the model and storage options.[1]
Related pages
External links
References
- ↑ 1.0 1.1 The geneland development group (2017). Population genetic and morphometric data analysis using R and the Geneland program. http://www2.imm.dtu.dk/~gigu/Geneland/Geneland-Doc.pdf. pp. 6–9. Search this book on
- ↑ Guillot, Gilles (2005). "Geneland: a computed package for landscape genetics". Molecular Ecology Notes. 5: 712–715.
Resubmitions, formating edits
This article "Geneland" is from Wikipedia. The list of its authors can be seen in its historical and/or the page Edithistory:Geneland. Articles copied from Draft Namespace on Wikipedia could be seen on the Draft Namespace of Wikipedia and not main one.
