We have developed and in most cases, published, several software packages to support our analyses in landscape connectivity and landscape genetics research. All of these use the statistical and scientific programming language R in one way or another.
MEMGENE is a package for R that can detect relatively weak spatial genetic patterns using Moran’s Eigenvector Maps (MEM) to extract only the spatial component of genetic variation. It has applications in landscape genetics where the movement and dispersal of organisms are studied using neutral genetic variation.
It is available on CRAN, and has been published with tutorials and extensive supplementary material in Methods in Ecology and Evolution.
The analytical aspects of MEMGENE were developed in collaboration with Pedro Peres-Neto (UQAM).
ALLELEMATCH is a package for R that identifies unique genotypes and is particularly helpful for non-invasive sampling applications (e.g. where fecal or hair material is collected). ALLELEMATCH is available on CRAN and is published in Molecular Ecology Resources and has been applied for a range of applications including to support genetic capture-mark-recapture, to identified plant clones and to match tadpole samples to adult frogs.
GRAINSCAPE is also an R package for developing grains of connectivity and minimum planar graphs of landscape connectivity. A detailed tutorial is available here. GRAINSCAPE is hosted at the secondary R repository, R-forge and thanks to Andrew Fall is distributed with his binary, SELES. Instructions to download, install, as well as manuals and tutorials are available here.
Although it has not itself been published in a journal, it is used in three papers (Galpern et al., 2012, Molecular Ecology; Galpern & Manseau, 2013, Landscape Ecology; Galpern & Manseau, 2013, Ecography).
POPSCAPE is a landscape genetic simulation engine written partly in R and partly in the agent-based modelling framework NetLogo. It enables the programming of agents (representing individuals and their genes) and allows them to move and mate anywhere within a pre-defined world.
A resistance surface, describing the hypothesized influence on gene flow by landscape features can be included. Demographic and vagility parameters can also be manipulated. It is used and presented in an appendix of the MEMGENE paper in Methods in Ecology and Evolution. If you would like to use this code, please get in touch.
MicroSatServer is a database web application that with collaborators Micheline Manseau (Parks Canada & University of Manitoba) and Paul Wilson (Trent University), we use to manage and coordinate genetic data for almost 10 000 caribou fecal pellet samples. The link contains a PDF summarizing its features. If you are interested in developing your own version of MicroSatServer, please contact me, and I will share source code!