Hi @brett,
Welcome to the 
forum!
There's a simple answer and a more complicated one. The direct answer to your question is to import the aligned sequences and use RESCRIPt to degap and filter.
My (entirely unsolicted) advice would be to denoise before you do clustering since it's better than your standard quality filtering. If you're combining multiple regions in different samples (one region / sample), closed reference picking is the way to go. If you're combining multiple regions within a single sample, some work I did recent suggests that sidle is the most accurate option and plays pretty nicely with most databases. (With multiple regions in a single sample, and a specialized database you're likely to get trustworthy species level resolution.)
Best,
Justine