change in rarefaction output

Hi Pat,

It has been a while since I ran rarefaction analyses and I noticed that the results are now rounded to the nearest species whereas they used to be expressed as decimals to 3 places. Is there a reason for this? This makes the curves much less smooth when plotting them, at least with some of the smaller libraries I am working with.

Thanks, Jesse

I think we’re reporting the median now (i.e. 50th percentile) instead of the mean. This should really only be an issue if you have small datasets.

It also makes the curves less smooth if you have very low diversity communities (I have ~30 OTUs in a MiSeq dataset of 260,000 sequences). Is there a place where I can get the mac executable for the most recent version of Mothur that still reports the mean?

Solved. I don’t know what the most recent version that still reports the mean, so I randomly choose one in the past. I installed version 1.27 (August 2012) and my curves look much smoother now!