How will mothur handle a distance matrix that contains -1.0 when it is used to cluster reads? Dnadist outputs -1.0 when sequences are too far apart to get an accurate distance measure between them. Are only non-negative distances considered, or will these outliers be clustered closely with the sequences that are 0.0 apart?
Distances of -1 are ignored by mothur, so in effect it’s like setting the distance to infinity.
Will the distance of -1.0 interrupt downstream commands such as rarefaction.shared and get.sharedseqs? I’m having an issue with this and suspected it was the 1’s in the distance matrix.
These distances are treated as infinity. They shouldn’t affect downstream processing. However, you might be more concerned about why you have such distances and I suspect that you don’t want them. Basically, you will inflate the number of OTUs you have by including these distances. Such distances occur when the sequence alignments do not overlap. You want all of your sequences to overlap over the same region. If you want us to take a look at the distance file for you, please forward it to firstname.lastname@example.org.
Hope this helps,