Information on classify.seqs cutoff

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amwalkero0o
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Location: University of Alaska Fairbanks

Information on classify.seqs cutoff

Post by amwalkero0o » Thu Feb 08, 2018 2:23 pm

Hello,

I am wondering if there is a specific paper or collection of papers that you are referring to in the classify.seqs cutoff section stating "The current thinking seems to be to use a minimum cutoff of 60%. Mothur's default is set to a value of 80%"? If so, could you point me towards them? I am having trouble understanding how these cutoffs are determined and what makes the most sense for my data.

**Edit: The Mizrahi-Man et. al. 2013 paper seems to cover this, however I am realizing my lack of understanding lies in why one would choose an 80% threshold over 90% or 95%? Is it because a higher % is more precise than what we can realistically classify?

Thank you in advance!

pschloss
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Re: Information on classify.seqs cutoff

Post by pschloss » Mon Feb 12, 2018 3:52 pm

The 80% likely comes from the phylogenetics literature where people are generally content with 80% bootstrap support.

Pat

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