When is a not updated software considered deprecated in the academic world? Currently I'm writing a thesis in Computer Science for which I need to introduce and compare several open source tools that are available for performing a certain type of testing (mutation testing) on some piece of code.

To reduce the number of tools (initially  more than 25), I set two limits : 


The tool must have been updated in the last 5 years to be present in the list, otherwise it is considered obsolete.
Only tools that work for one of the 3 most used languages are considered. I defined them with the TIOBE index (Java, C/C++ are equivalent for the tools and Python).


I arbitrarily set the first condition to five years, but I would not be able to justify this number if needed. I didn't find a study or article with a point of view on the subject.

So my question is: After how many years without updates would such a software (or any software) be considered deprecated?
I don't think there is such a standard, certainly not one applicable to all of academia. For your thesis, I would suggest that it might be more useful to talk about "recently updated" / "currently developed" software, rather than labeling the rest as obsolete.

"Deprecated" signals that the creator no longer recommends using the software. I can't think of any real examples for a full software package (i.e. going beyond deprecating part of an API), but I guess it might happen if the software is known to produce bad results.

Software might be "obsolete" if it has been de facto replaced by a better option, but certainly not just because it's old. Even then, the old option might be good enough. Visit a couple of (established) experimental labs in the sciences, and you'll likely see lots of old equipment still running old software. Changing it all out would just be needless overhead, and not be guaranteed to help. There's almost always a better place to spend the money you might have... From another angle, if you consider numerical algorithm implementations and libraries as tools, there's a number of them that have gone decades without updates, yet are still routinely imported and used in new software development.