I need to cluster sequences with 30-40% of identity threshold. Which tool would you recommend?
I've tried CD-HIT, but it's not recommended for such low identity. I was also searching for clustering with identity threshold in MUMmer, kalign and clustalO, but I could not find it.
Any help would be much appreciated!
Edit: I have two types of input files to cluster, basic fasta file with multiple sequences and aligned fasta file (kalign).