I’m working on a dataset which consists of sequences with 800 to 1000 bases. I use align.seqs and the silva database file you supply (silva.nr_v119.align).
mothur > align.seqs(candidate=XXX.fasta, template=silva.nr_v119.align, processors=2)
The sequences I get are very short (around 5 bases) or contain only dots.
Why does mothur delete my bases and how can I prevent this?