One trick that is sometimes necessary to run Linux binaries under FreeBSD is to fool the binary into thinking it is running on Linux. Sometimes the binary will complain "This isn't Linux -- can't run" and you then have to say, "Sure -- this is Linux -- trust me!" For example, Matlab and Maple both complain that they don't support FreeBSD when you try to run them. By using a compatible shell, they can be tricked into running on FreeBSD. This typically consists of changing lines in a shell script, e.g.

#!/bin/sh

to

#!/compat/linux/bin/sh

and then commands like uname will return "Linux" etc., and the binary runs without problem.