When cluster cutoff changed, go on or change method?

Commands in mothur
1

Hi,
As cutoff often changed when use cluster, should I go on or change method? By default cluster () uses the average neighbor algorithm.
Thanks in advance! :slight_smile:

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Here’s Pat’s explanation about why the cutoff changes, http://www.mothur.org/wiki/Frequently_asked_questions#Why_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F We recommend the average neighbor method. You can always adjust the cutoff slightly higher, but if you are still clustering to unique, then this might be the issue, http://www.mothur.org/wiki/Frequently_asked_questions#Why_is_my_dataset_only_clustering_to_.22unique.22.3F or this http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix%3F/