Im using now using mothur for quite a while and it is really handy and flexible program to
filter and analyse your sequence data.
However there is a command that i really need and is not (not yet found) available.
This is how i would call it: the global.summary command.
Its a total summary where per row a unique otu (or dist otu like 0.03) including sequence frequency per sample;
taxonomic lineage and fasta sequence (that is used in clustering and classification).
Otu sample 1 sample 2 sample 3 taxonomic lineage fasta
1 1000 500 0 bacteria etc etc. ACGTACGAGTCAGTCGAT
2 0 200 300 bacteria etc etc. ACGTACGAGTCCCAATTT
This would make our analyses alot easier. I hope this is possible because all the information is in the fasta, list, taxonomic, group and name files.