Software

Zonation
Virtual Migration Model
Stochastic patch occupancy model
Simple connectivity model
Testing for inequalities among loci
Validation of Phylogenetic trees from microsatellite data
B-Range - a program to analyse animal movements and home ranges
RSW - Reserve Selection with Weights

Zonation v. 1.0 - A spatial conservation planning software, which can be used to identify sites important for species conservation. Zonation produces a hierarchical prioritization of the landscape based on the biological values of sites (cells). The software includes several practical features such as aggregation methods, uncertainty analysis, species prioritization and replacement cost analysis for current or proposed reserves. The data requirements are realistic and Zonation can analyse relatively large data sets in reasonable time. Windows software package includes user manual and tutorial. The software has been written by Atte Moilanen. Read more and download the software here .

Virtual Migration Model

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.

Stochastic patch occupancy model

SPOMSIM 1.0 . Beta version of the large metapopulation analysis software package for windows. Includes e.g stochastic patch occupancy model definition, simulation, parameter estimation, patch system editing, reserve network design etc. The software has been written by Atte Moilanen.

Simple connectivity model

Si ; a program for calculating simple connectivity measures from metapopulation data. See Moilanen and Nieminen 2002. The software has been written by Atte Moilanen.

Testing for inequalities among loci

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.

Validation of Phylogenetic trees from microsatellite data

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.

B-Range - a program to analyse animal movements and home ranges

B-Range was build to analyse a specific data set of bears composed of radiolocations with irregular time interval. Although the program was not designed for public use, it can also be used with other data sets. With B-Range you can estimate areas used by an animal with MCP, kernel and time kernel methods, and output the habitat composition of home ranges (both UD weighted and "flat"). This Windows based program is constantly under development, but you can download current version 2.0 here. In case of any questions you can contact Jonna Katajisto (jonna.katajisto(at)helsinki.fi).

RSW - Reserve Selection with Weights

RSW is a program for solving maximum coverage -type reserve selection problems. It utilizes forward and backward heuristics and simulated annealing for finding near-optimal solutions to the problem. This program introduces several novel features in reserve selection: (1) species weighting, (2) benefit functions for representation, (3) species-area-based refinements and (4) replacement-cost analyses. Installation package includes a pdf documentation, an alternative .chm help file (read either one, both have same contents) and example files for tutorials. The software has been written by Atte Moilanen .RSW_v1.1.zip.