The license information, rights of use and additional information can be found under each individual program entry or from the readme file within the program download.
RAFM and driftsel
RAFM and driftsel are Bayesian R packages for evolutionary quantitative genetics. RAFM can be used to estimate population genetic structure from neutral marker data. driftsel combines the output of RAFM with quantitative trait data to examine if trait divergence can be explained by the null hypothesis of neutral drift.
Hierarchical Modelling of Species Communities (HMSC) is a model-based approach for analyzing community ecological data. HMSC partitions variation in species occurrences to components that relate to environmental filtering, species interactions, and random processes.
More information and downloads of the program.
Zonation is a conservation planning framework and software. It produces a hierarchical prioritization of the landscape based on the occurrence levels of biodiversity features in sites (cells) by iteratively removing the least valuable remaining cell while accounting for connectivity and generalized complementarity. The output of Zonation can be imported into GIS software to create maps or for further analysis. Zonation v. 4.0 can process very large data sets containing up to ~50 million grid cells with effective data.
Zonation identifies areas important for retaining habitat quality and connectivity for multiple species, indirectly aiming at species’ long-term persistence. The computational strategy of Zonation can be characterized as maximal retention of weighted, range size normalized (rarity corrected) richness. Zonation produces a complementarity-based priority ranking.
Zonation quick introduction manual (approx 30 pages)
Running Zonation projects manual (approx 60 pages)
Full download, including software, manuals, presentations, and example setups (300 Mb .zip file)
RobOff is software for (non-spatial) targeting of alternative land use options, when actions have variable costs and different effects over time. RobOff comes from Robust biodiversity Offsetting, one of the uses of the software.
Roboff download, including software and manuals
Probabilistic taxonomic classification software.
A grid/patch based metapopulation model for dynamic landscapes, implementing methods in Hodgson, J., Moilanen, A., and C. D. Thomas. 2009. The responses of butterfly metapopulations to patch connectivity and average patch quality are masked by successional habitat dynamics. Ecology 90: 1608-1619.
RSW2 is a program for solving maximum coverage -type reserve selection problems, where one seeks to maximize conservation value obtained with a limited budget. The novelty in this program is that the conservation value of a reserve network is not merely the number of species represented in it, but is derived using several optional features that make conservation planning more realistic. These include differential species weights according to their conservation priority, continuous benefit functions for species representation, refinements for site size based on the species-area relationship and combining quantitatively site value (replacement cost (by christinaat dhead)) with urgency of protection (vulnerability). The software calculates replacement costs for sites, which is a type of irreplaceability measure based on the use of continuous benefit functions. More information from the Conservation Biology Informatics Group pages (currently not working).
SPOMSIM 1.0 . Software for the analysis of SPOMs, Stochastic Patch Occupancy Models of metapopulation dynamics. Includes e.g SPOM definition, simulation, parameter estimation, patch system editing, reserve network design etc. The software has been written by Atte Moilanen.
AnimalFarm ver. 1.0 performs the statistical test for unequal contribution of loci to microsatellite SMM based distance coefficients [such as Goldstein’s (dm)2 or Slatkin’s Rst]. From individual genotypes provided in a separate input file, AnimalFarm computes the Fctr ratio for every locus and assess its significance by permutation. Details of the methodology can be found in Landry PA, MT Koskinen & CR Primmer (2002) Deriving evolutionary relationships among populations using microsatellites and (dm)2: all loci are equal, but some are more equal than others... Submitted to Genetics.
MsatBootstrap ver. 1.1 is a program for bootstrapping microsatellite loci data to derive and validate phylogenetic relationships among populations. This program is meant to be used in conjunction with the phylogeny programs of the Phylip package (Felsenstein 1995). From individual genotypes provided in a separate input file, MsatBootstrap performs the bootstrap resampling of microsatellite loci and calculates 2 interpopulation distance coefficients (i.e. Goldstein's ( dm ) 2 or Slatkin's R st ) to recover the phylogenetic relationships among populations. In addition, MsatBootstrap allows the user to standardize the allele sizes following Goodman (1997). Results from different distance indices are written in separate output files that can be directly analyzed with the Phylip programs.
Virtual migration model ( VM ) estimation and simulation. A novel method for estimating parameters of migration and mortality in patch and during migration from standard mark-recapture data. Unzip with pkunzip option -d to recover directory structure in package. See included readme-files for details. Instructions for using the virtual migration programs based on I. Hanski, J. Alho and A. Moilanen. 2000. Ecology 81, 239-251. The software to parameterize the model and simulate metapopulation dynamics with it has been written by Atte Moilanen.