distance cutoff in the clusters

Commands in mothur
1

Hi Pat, Sarah, and other mothur users,

I have started enjoying using mothur for re-processing my old V6 pyrosequences. By no means I’m familiar with all the commands, but here is a problem I have run into:
After alignment, I used mothur to generate a column distance file with the cutoff = 0.07. I checked the dist file and found it was okay, containing distances from 0.000 to 0.069. Then, I read in the dist file (read.dist) with the name option before I clustered the sequences with average neighbor method. In the sabund/rabund/list files I only found distances unique, 0.01, 0.02 and that’s it. My goal is to do analysis with the 0.06 distance. Where would I find them, or what could I have done wrong…?

2

If you’re doing average neighbor then you probably will need to set the cutoff in dist.seqs to 0.20.

Pat

3

It worked after I increased the cutoff to 0.20. Thanks for your suggestion.