After using the filter.seqs command to reduce the number of uninformative positions and get the representative OTUs with the get.oturep command, is it possible to reverse the effect of the filter.seqs command and get the original number of positions (present in the greegenes database for example)? I would like to import the representative OTU in Arb. I can realigned the fasta’s containing the representative otu but it is not really convenient.
Thank’s in advance
The easiest way to do this would be to generate a list of sequence names you want and then run get.seqs using the original alignment as your fasta file
Thanks for the answer, but I found that not applying the filter.seqs command is in the end faster that trying to get back to the original number of positions.
Realize that will also have some unintended consequences - you will no longer only be comparing like to like since your sequences will be different lengths and overlap different alignment positions.