precision in cluster and dist.seqs

Commands in mothur
1

Hello Pat,

Why does my precision skip 0.00 and 0.03-0.005?

mothur > cluster(phylip=TA_2.unique.filter.good.filter.phylip.dist)


You are using a phylip file and no cutoff. I will run cluster.classic to save memory and time.

/------------------------------------------------------------/
Running command: cluster.classic(phylip=TA_2.unique.filter.good.filter.phylip.dist, precision=100, method=average, hard=T, sim=F)
********************###########
Reading matrix: ||||||||||||||||||||||||||||||||||||||||||||||||||||

unique 2 31 2
0.01 17 11 2 1 0 0 0 0 0 1
0.06 17 10 1 2 0 0 0 0 0 1
0.07 18 7 2 2 0 0 0 0 0 1
0.08 18 6 2 1 1 0 0 0 0 1
0.09 18 5 1 2 1 0 0 0 0 1
0.10 22 4 0 3 0 0 0 0 0 1
0.11 23 2 0 2 1 0 0 0 0 1
0.16 23 1 0 2 0 1 0 0 0 1
0.17 28 1 0 2 0 0 0 0 0 1
0.19 29 0 0 2 0 0 0 0 0 1
0.22 32 0 0 1 0 0 0 0 0 1
0.24 35 0 0 0 0 0 0 0 0 1

Output File Names:
TA_2.unique.filter.good.filter.phylip.an.sabund
TA_2.unique.filter.good.filter.phylip.an.rabund
TA_2.unique.filter.good.filter.phylip.an.list

It took 0 seconds to cluster
/------------------------------------------------------------/

Thanks!

2

Because there weren’t any changes to the clustering between 0.01 and 0.06. So if you want to know what to use for 0.03 or 0.05, you should use 0.01. This commonly happens with small datasets like yours.