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Though I know there is some MS-Windows based software which is used in ecological science (there is even a branch environmental informatic), I know only Ecolab available for Linux yet. But I guess Linux software (for instance databases or statistics programs) may easily adopted. Also it might be possible to use a Linux cluster to solve ecological simulations.
Ecolab is both the name of a software package and a research project that is looking at the dynamics of evolution. EcoLab is a system that implements an abstract ecology model. It is written as a set of Tcl/Tk commands so that the model parameters can easily be changed on the fly by means of editing a script. The model itself is written in C++.