Screening by query name

Is there a way to screen out sequences by their name?

I have outgroups that are undetected until I build the tree. They are non-target sequences that will form their own clusters and create spurious OTUs. I know I can delete them from the fasta file manually and rerun everything, but it would be nice if I could just screen them out with a single command and update the associated files at the same time.


If you make a file that’s just a list of the reads you want to remove, you could use the remove.seqs() command:

remove.seqs(fasta=final.fasta, name=final.names, group=final.groups, accnos=yourlist.txt)