pre.cluster and aligned vs. unaligned sequences

Quick question:

As I understand it, the pre.cluster algorithm is designed for use on multiple sequence aligments. Is there a reason that it should or should not be used on unaligned sequences, either instead or as a pre-alignment step?

Thanks in advance,
Craig Nelson

Great question. pre.cluster does not do an alignment, it uses the input alignment. So if do not align your sequences and they have insertions/deletions, they will not be detected and will shift your entire sequence. Although we could incorporate pairwise alignments into pre.cluster to detect in/dels, it would be a lot slower than doing align.seqs followed by pre.cluster.