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Old 01-08-2010, 08:18 AM   #1
Location: Montreal

Join Date: Oct 2009
Posts: 63
Default Rarefaction distance explanation

I have 16s data (target: 96F 1492R) that was run on 454. The results are very good. I used ESpirit and mothur on the data to get Chao1 good's coverage and rarefaction graphs.

I was just wondering if any one of you knows of a publication/books which goes into details explaining why the distances 0.01, 0.03-0.05, 0.1 are very 'important' as diversity markers.

I deduced that 0.01 means that the OTUs are of the same species
0.03-0.05 are of the same family/genus
0.1 same phylum/class

But I can't find any clear cut study on those numbers.

lletourn is offline   Reply With Quote
Old 01-28-2010, 12:57 PM   #2
Senior Member
Location: Ohio

Join Date: Jan 2010
Posts: 144

I think those are just heuristics. I have heard 1% for strain/subspecies and 3% for species, but those definitions are fluid.

Here is a review:
Pace, N. R. (2009). "Mapping the tree of life: progress and prospects." Microbiol Mol Biol Rev 73(4): 565-76.
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Old 03-11-2011, 09:09 AM   #3
Location: Montreal

Join Date: Oct 2009
Posts: 63

I know you answered this awhile ago, but thanks a lot, it's exactly the kind of article I was looking for.
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