why cut off changes at dist.seqs step ??

Commands in mothur
1

Hello,

why cut off changes at dist.seqs step ?


This is what I saw:- mothur > dist.seqs(fasta=filtered.precluster.pick.pick.fasta, cutoff=0.20)

Using 4 processors.

Output File Names:
filtered.precluster.pick.pick.dist

It took 36 to calculate the distances for 5067 sequences.

mothur > cluster(column=filtered.precluster.pick.pick.dist, count=filtered.precluster.uchime.pick.pick.count_table)
********************###########
Reading matrix: |||||||||||||||||||||||||||||||||||||||||||||||||||

changed cutoff to 0.107221

Output File Names:
filtered.precluster.pick.pick.an.unique_list.list

Looking forward,
Richa

2

It is actually changing in the cluster step:

http://www.mothur.org/wiki/Frequently_asked_questions#Why_does_the_cutoff_change_when_I_cluster_with_average_neighbor.3F

3

Thanks for the explanation :slight_smile: