not all pairwise distances with dist.seqs


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


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!

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.

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.