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Canoco for Windows is the next generation of Canoco software, the most popular tool for constrained and unconstrained ordination in ecological applications. Canoco for Windows integrates ordination with regression and permutation methodology, so as to allow sound statistical modelling of ecological data. Canoco for Windows contains both linear and unimodal methods. Ordination diagrams can be displayed on screen immediately after an ordination has been calculated. Canoco is unique in its capability to account for background variation specified by covariables and in its extensive facilities for permutation tests, including tests of interaction effects. These unique features make Canoco for Windows particularly effective in solving applied research problems. Canoco has been designed for ecologists, but Canoco has also been used in toxicology, soil science, geology, archeaology, water district management, food and health and public health research and market research, to name a few.