R (Windows, MacOS, Linux, Unix)
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.
Based on the S language, this is similar to S-plus software. It may require a steep learning curve initially, especially for those not familiar with command line programming, but the benefits will usually outweight the effort.
There is an impressive set of packages for analysing genomic data and these are commonly known as BioConductor. Both R and BioConductor are open source, have excellent documentation and have active and helpful mailing lists.
Further details are available from