Geneland
Geneland[edit]
| Geneland | |
|---|---|
| Developer(s) | Gilles Guillot |
| Written in | Fortran, R |
| Operating system | Windows, Linux, MacOS |
| Website | www2.imm.dtu.dk/~gigu/Geneland/ |
Geneland is a computer software created by Gilles Guillot used as a package of the free statistical software R or as a software with user friendly interface. The software is computing spatial statistical model on population genetics data. It clusters your data into a certain number of populations (groups) where each of the population is homogeneous. The clustering is based on phenotypic data, spatial data and genetic data.
The software is possible to run on Windows, Unix and MacOS. The core of Geneland is written in Fortran and only little knowledge of R is needed to run it..[1]
The main functions of this software is to use a georeferenced individual multilocus genotypes data to decide the number of populations and of 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 variable by Dirichlet model or Falush model.[2]
As a results, user can get plots containing spatial distributions of individuals, maps showing into which population is each individual belonging based on phenotypic data, spatial data and genetic data. Combining Geneland with other R packages, such as RgoogleMaps, user can get as a result Google map with 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 100000 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 a storage options.[1]
Related pages[edit]
External links[edit]
References[edit]
- ↑ 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[edit]
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