If you're using Linux or MacOSX you definitely want to try the BIRCH system.
See the BIRCH Multiple sequence alignments tutorial which shows how to eliminate redundant sequences using CD-HIT.
You can learn more about BIRCH on our YouTube channel at https://www.youtube.com/channel/UC9_3TfH3sjE0YdToVMChq-w?view_as=public
There are numerous software tools for this problem. None of them is a standard or so much better than the others that one would definitely want to try it.
By the way, there are numerous links on the right side of this page that probably answer the poster's question.