I’m using mothur to create rarefaction curves but I have the following problem:
I load the distance matrix (read.dist(phylip=fasta_GT2.dist, cutoff=0.1)), run the cluster command (cluster()) and get the *list file. This *list file, however, always contains OTUs of predefined distances, ie 0.00, 0.02, 0.05, 0.07 etc.
Is there any way that I can change these values so that, for example, it can calculate the 0.03 distance?
From the wiki: http://www.mothur.org/wiki/Cluster
" Missing distances
Perhaps the second most commonly asked question is why there isn’t a line for distance 0.XX. If you notice the previous example the distances jump from 0.003 to 0.006. Where are 0.004 and 0.005? mothur only outputs data if the clustering has been updated for a distance. So if you don’t have data at your favorite distance, that means that nothing changed between the previous distance and the next one. Therefore if you want OTU data for a distance of 0.005 in this case, you would use the data from 0.003. "
Thank you for your help!!