VEGAN adds vegetation analysis functions to the general-purpose statistical program R. Both R and VEGAN can be downloaded for free. VEGAN implements several ordination methods, including Canonical Correspondence Analysis and Non-metric Multidimensional Scaling, vector fitting of environmental variables, randomization tests, and various other analyses of vegetation data. It can be used for large data. Graphical output can be customized using the R language's extensive graphics capabilities. VEGAN is appropriate for routine and research use, if you are willing to learn some R.
Abbreviation: MDS = Multidimensional Scaling.