taxonomic distribution of samples

Commands in mothur
1

Hi,
I am once more stuck in my analysis and require some help…
After following the 454SOP until classify.otu (in “preparing inputs for analysis”), I would like to use the shared file and the taxonomy file to produce an histogram of the taxonomic diversity. I mean 1 column per sample (group), and within the columns the % of presence of OTUs, better at the phylum level.
How can I do that? I could do it manually (arggg), but I guess there must be a way of doing it using only few commands… All the tutorials I saw focus on statistical analysis, but I could not find anyone explaining this basic step.

Thanks a lot.

2

So try this…

phylotype( use level=6 -> phylum )
make.shared
classify.otu

That will give you a phylum level shared file and the taxonomy information.

Pat

3

Thanks a lot,
of course it was in the SOP, but I did not understand it that way.
Regards.