I do not agree with the explanationless downmod of this question. Yes, it is basic (and maybe phrased plain wrong) but so are a lot of other ones here that do get contructive comments. I think DK Shetty should not generally be discouraged asking these types of things, especially since he is new to the site. On the other hand, he should have put more effort into phrasing a proper question.
As a response to Nico's answer: In my mind, two things can be compatible or not no matter in which order they are put in the sentence. Thus, if A is compatible with B then this implies the other way around. Also, the issue is a little bit more complicated than you outlined here.
Basically, the source code of a programm can be built for a certain architecture (eg. i686 for standard 32bit processors or x86_64 for standard 64bit processors (simply put). The executable (=built program) can be run within the same architecture. How many cores your processor has does not really matter in the case of the mere possibility of code execution.
However, with the rise of multi-core CPUs, programs need to have certain properties in order for them to be executed efficiently. For instance, modern hardware can process a multitude of threads at the same time. If the program spawns only one thread, it does not make full use of the hardware, even if it was compiled on that specific platform.
That being said, most of the up-to-date tools make extensive use of parallel thread execution. In some cases, there are specialized modifications of them in order to run them efficiently in a distributed environment (eg., MPI for clusters) or the the graphics processor (GPU, eg. CUDA).
As to UNIX vs. Windows tools: most of bioinformatics happens on Linux, for a multitude of reasons. Most web servers run some flavor of Linux and so do almost all computing clusters. The "real work" (read: contig assemblies, microarray analysis, and really everything with a large data volume; this is compared to commercial graphical end-user interfaces) is being done here. So the question in most cases is, how good are their Windows ports?
edit: a little rephrasing