I have a miseq 16S dataset, ran thorugh the SOP and run dist.seqs and then clearcut as in the SOP but when looking at the tree (in Genious and in Phyloseq) I see one very long branch that sticks out from everything else. I blasted a few sequences and only got good matches from the databases; I extracted part of the alignment with sequences from within and outside the cluster and couldn’t find anything wrong with the alignment, and I made a new NJ tree in Genious (without realigning) and there was nothing special about the tree that came out - the sequences that were in the strange cluster in the mothur tree do cluster together but are not sticking out at all from the rest of the tree.
Is this normal? Is the long branch length for that cluster irrelevant? If not, is there a way to fix it in mothur?
Thanks for the help,