C is still the language of choice for this kind of tools. If you are capable of writing a high performance string matching tool ...
I know that, and that is why I asked that question. Is it worth to spend >1 year coding a "very efficient suffix array tool" when (maybe) you can code it in less time being less efficient but in a language that supports parallel and concurrent computation (ideally) easily?
The point about memory is relevant, but I don't know if critical in this case (I'm not trying to build suffix arrays over strings of 3Gbs)
Thanks for your reply,