Cluster.split by classification

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?


Hi Tris,

It would consider the higher orders - so if you have a bunch of order level “unclassifieds” but they come from different classes, then they would be split into separate groups by class.

As for large=T, I’m not sure what is going on there. However… we’ve found the large=T option to be a disaster for the average neighbor algorithm. It ends up sucking up more memory than the large=F option and so it’s hard to imagine a case where you’d want to use large=T.