Past is free software for scientific data analysis, with functions for data manipulation, plotting, univariate and multivariate statistics, ecological analysis, time series and spatial analysis, morphometrics and stratigraphy.
EstimateS is a free software application for Windows and Macintosh operating systems that computes a variety of biodiversity statistics, estimators, and indices based on biotic sampling data. Some features require species relative abundance data, others only species presence/absence data. A comprehensive User’s Guide is available online at this site.
R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.