I’m studying the fungal community on decaying roots using 454 pyrosequencing data. To deal with the pyrosequencing error, I want to precluster my sequences before clustering. I have a few questions on the pre.cluster command in mothur:
Can the pre.cluster command work on sequences that are not aligned ? (my sequences cannot be aligned since they are from universal fungi)
Is there a mothur precluster command that is based on the distance matrix ? I have got the distance matrix (distances between unique sequences) by running unique.seqs and pairwise.seqs.
On the mothur manual (the Pre.cluster page), given that one has already aligned,filtered and uniqued the sequences, why unique.seqs needs to be run again before running the pre.cluster command?
Thank you !