Quality of clustering: Cluster.split versus Cluster commands

Dear mothur community,

Since I had a distance matrice too large (315 Gb) to load it in the RAM of my server (126 Gb of RAM), I used the cluster.split command with a classification based on the fasta (taxlevel=3), and the opticlust algorithm. It went smoothly and I succeed to reach the OTU table step.

Now, I would like to know the implication of this alternative method in terms of clustering quality ? And how to manage it properly in the rest of the pipeline and interpretation of the results.
I believe to already read something about it through a previous post in the forum, but I cannot find it back… also I apologize for an eventual duplicated topic.

Thank you,


It should be just as good. Well, in a way, it’s better - because before you had nothing :slight_smile:

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