not all pairwise distances with dist.seqs

Commands in mothur
1

Hi,

I wanted to get all pairwise distances (in table format) for the representative sequences of my OTUs (clustered at 0.030). So, for this I first ran

get.oturep(phylip=final.pick.pick.square.dist, fasta=final.pick.pick.fasta, list=final.phylip.fn.pick.pick.list, cutoff=0.030, label=0.030)

Then I ran the dist.seqs command on the new new fasta file with the representative sequences

dist.seqs(fasta=final.phylip.fn.pick.pick.0.030.rep.fasta, calc=eachgap, cutoff=0.030)

The output looked correct, but the weird thing was that it didn’t contain ALL the pairwise distances for the sequences. However, running

dist.seqs(fasta=final.phylip.fn.pick.pick.0.030.rep.fasta)

This gave me ALL pairwise distances BUT the distances are not correct (not the same as in the above output) since they are in the size of 0.3-0.4 while they should not be above ~0.03 since that’s the threshold I’ve used to cluster at.

Any pointer on this discrepancy would be highly appreciated, thanks!

2

The sequences within an OTU are going to be on average less than 3% different from each other. In contrast, the distance between OTUs should be greater than 3%. So your result seems to make sense to me.

3

Hi Pat,
Thanks for the reply. You’re of course absolutely right. The distances between OTUs should obviously be greater than 3%. Don’t know what I thought here. Sorry for unnecessary post.