To apply or not to apply, that is the question...
If you meet a majority of requirements for a position, but aren't familiar with a software application or two-- don't let it stop you. Here's a quick remedy from a familiar source:
Aspiring comedians, actors, and singers all use YouTube as a medium to market their skills, and fortunately for you--so do technical trainers.
Simply do a search on the name of the application you need to learn and you'll likely find a menu of short training videos to choose from.
Watch the trainings, take notes and--when possible--practice using the real application.
If it all goes well and you feel confident that you'd be able to use your new skill in a work environment, write the name of the application on your resume and say "Familiar with ______________."
(Don't say that you are proficient in an application until you feel comfortable that you could pass a user's test on it...you may be tested during the actual interview process and you don't want to misrepresent your skills.)