Do you know what it would be really awesome if Mothur did?
Sub-sampled Fasta files to the same number of sequences so that comparisons between samples aren’t biased due to different sampling efforts.
Currently I use daisychopper (http://www.genomics.ceh.ac.uk/GeneSwytch), but it would be great if I could just add this to my Mothur pipe line.
Just a thought…
Keep up the great work
Yeah, it’s in the works. However… I think that if people stay away from beta-metrics based on counts (i.e. Bray-Curtis) this shouldn’t be such a problem. The next version of mothur will have something kind of like you want. We’ll have a command that converts the output of get.relabund to a shared file where every line has about the same number of sequences. If you’d be interested in giving this a whirl, pre-release, let us know (firstname.lastname@example.org).