Unclassified sequences

Commands in mothur
1

We are interested in doing additional analysis on sequences that are unclassified by classify.seqs. We would like to do some manual BLAST and alignments to determine if they represent novel taxa. Is there an easy way to obtain the sequences themselves and information about which samples they were found in, starting from the fasta, taxonomy, names and groups files?

Thanks in advance.

2

You can do get.lineage and use taxon=unclassified to pull out those reads that are unclassified.

3

Thanks - that is what I need.