I don't think the words "trade secret" fit - the correct term is "Intellectual Property" (IP).
[nerd mode] Just to be boring, a "trade secret" is a type of Intellectual Property. You can patent an invention - but that means making it public. However, software can't normally be patented, and algorithms can be hard to patent. Software implicitly has copyright, so others can't copy it directly (I mean byte by byte). But if someone figures out what it's doing, there's nothing to stop them writing their own software that does the same thing. So sometimes it's easier to keep software IP as a trade secret - just like the formula for Coke. This is often the case with software that's buried in a box. [/nerd mode]