Hey all! I have a number of plasmid sequences (119) from 500 to 170000 base pairs long. Some of those sequences are redundant, but that redundancy is only identifiable through alignment, there are no descriptors to sort out redundant sequences.

What I want to do now is to cluster these sequences after similarity, to sort out redundant sequences in later steps. I tried uclust, but I think it cannot handle the length of the sequences.

Can somebody recommend a tool or a way to do this?

Thanks!