Cluster complete plasmid sequences

[sequence_hard]

Hey all,
I have complete nucleotide sequences for 119 plasmids, with sizes ranging from 500 to 170000 base pairs. Is there a way to cluster those sequences such that I can sort out sequence redundancy? (for example, if a small sequence is covered to 100% in one of the bigger sequences, I want to recognize that in the cluster)

I have tried doing it in uclust, but I think it cannot manage the length of the sequences.
Can anyone recommend a good tool to do this?

Thank you!

[GenoMax]

For reference cross-posted: https://www.biostars.org/p/181585