What does my rarefaction output mean?
The first column represents the number of sequences, each of all other columns carries a header for all distance cutoffs starting 0.00 (0.00%) to 0.50 (50%) and represents the number of OTUs as the first column in the same row.
What do the U and L in the results stand for?
The "U" rpresents the upper bound and the "L" represents the lower bound.
What must I do before I can run the rarefaction tool?
First, you must align the sequences. Then, cluster the sequences using the alignment as the input. Use the resulting cluster file.