Creating Uniqueness In The Set Of Sequences

Question

[Pals]

Hello,

I would like to know how we can filter out the sequences that are more than XX% similar in a set of sequences? I have downloaded sequences from PFAM but there are groups of sequences that are highly similar if not conserved and I want to remove those sequences before making an alignment. Are there any such options in alignment editing programs (Bioedit, Seaview, Jalview,..)?

Thanks

Answer 1

[Chris]

CD-Hit is a commonly used program to filter on sequence identity.

[Pals]

Thanks Chris...

Answer 2

[Martin A Hansen]

Usearch/Uclust is well suited for this (better/faster than CD-Hit, but closed source :o/).