Quote from black diamond:
I use SAS and it is very good for this type of analysis, but I don't think it is cheap and it is not super quick to learn. I hear R can do the same stuff and is free but I have not used it.
R is an excellent software for this kind of analytical work. However its problem lies in database integration. Unless you can really dig deep into the dirty you cannot build a reliable RT data link between R and your database of choice. A friend of mine's fund somehow managed to pull it off but for individual traders it's better to stay with the proven commercial software such as Matlab or SAS. Yes it's kinda expensive but you get your money's worth. SAS can link up with SQL databases pretty well and Matlab is more powerful function-wise, but you have to build your own data link (much much easier than R though).