Unix or Linux application compatibility with X11 terminal/Mac OS X

I am an engineer and thinking about upgrading to a MacBook Pro. Most if not all of the applications that I use with respect to my work can be acquired in Linux or Unix flavors. I went to the local Apple store and requested that a "genius" install this software on a MacBook to take it out for a test drive. The "genius" was not able to install the application. Do I assume that the application cannot be installed, or that the "genius" did not know his stuff? I would really like to get the MacBook but want to be sure that my Unix and Linux apps will run on it. What is the compatibility issue here? Will any Linux or Unix app run on the Mac? Will the applications run only as command line or will a GUI be available? I need to hear from someone that knows the OS X.
MacBook Pro Mac OS X (10.4.8) thinking about purchase
Mac OS X (10.4.8)

I've worked with some pretty smart people, including Nobel laureates, and there are very few people I would say qualify as geniuses. It is unlikely they all work retail at Apple stores.
Anyway, what you are requesting is fairly standard. I made a web page to help you get going.
Briefly, you can run almost anything from Linux, but you have to compile it. There are free downloads for the compilers in Xcode, and X11 comes as a non-default install with the operating system (and the computer you would be buying). You can then either do it all yourself or use a package management system such as Fink or DarwinPorts (MacPorts?) in a similar way to how this is done on Linux.
There are some kernel-interacting linux applications that you might not be able to get to work, but I'd say well over 99% of what you would want will work fine. I use OS X as my primary scientific computing environment.
If you need Linux, you can install that too, and even run it in Parallels (a 3rd-party virtualization software that allows you to install windows, linux, or any other i386 OS).

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Despite extensive searching, I'm struggling with a font compatibility issue between my Mac and my colleagues' PCs. The main points in order:
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Andreas.
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Unix or Linux application compatibility with X11 terminal/Mac OS X

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