Cluster at average distance

Commands in mothur
1

I have som problems with the cluster command.
When I use the Furthest method to cluster, I got 4072 clusters, while I use the Average method to clust my sequences, there are 4371 clusters. As I can see, the Average method should be less stict than Furthest method. And there should be less clusters in the Average method than in Furthest. So how does it happen? Do I make some mistakes? My command line are as follows:
mothur “#read.dist(column=.dist, name=.names,cutoff=0.03);cluster(method=furthest,cutoff=0.03);”
mothur “#read.dist(column=.dist, name=.names,cutoff=0.05);cluster(method=average,cutoff=0.03);”

2

Can you double check that you’re looking at the right number. In the sabund format that goes to the screen, the number after the cutoff value is actually the number of sequences in the most abundant OTU, which would make sense in this case.

Pat

3

I got the OTU number from the second column of the list format file. And I have checked that the number is the OTU number.

4

So much for that idea - could you email your distance matrix and names file to mothur.bugs@gmail.com?