Hi Pat and Sarah,
Apologies if this has already been asked but I am wondering how the taxlevel argument works in the cluster.split function. If I have a bunch of seqs classified with many of them at order level being unclassified but spanning different classes and phyla, if I set the taxlevel to 4 would it group those unclassified sequences as 1 ‘split’ or would it consider the higher orders of taxonomy?
Also, as an aside, is there a reason cluster and cluster.classic no longer have the option to specify large=T? is this because of the cluster.split?
Thanks,
Tris