Distance to nearest neighbor (classify.seqs)

Hi Pat,
I’m trying to use mothur to link ARISA lengths to taxonomy using mothur. It’s really important to know how far the nearest neighbor is from the candidate sequence. Do you think you could add a column that says this match is XX distance or percent identity from the nearest neighbor.

Also, something that would be really helpful would be if I could choose to omit all sequences that are “Bacteria: Unclassified” from the taxonomy file. I can do this manually but an option in mothur would be really nice.

Loving mothur btw - your workshop over here at USC was awesome.


Thanks, Rohan. More output from classify.seqs is on the short list of features. You could also just merge the candidate and template and then run dist.seqs and then process the distances.

Hi Pat this ever get put into mothur?

Sorry - some how it slipped off of the list. It is officially on the list - now. Look for it in August.