Hi mothur forum,

may I have a reply on how to improve on unclassified
in the taxonomy file, if possible? For example, can
output from megablast become a taxonomy file?


blast is a pretty horrible way to do classification.

To improve the number of unclassified you can try…

  1. Change your database - use greengenes, silva, and rdp and see which works best
  2. Trim the database to the region you are interested in
  3. Get longer reads
  4. Pick a different region of the gene that will result in better classification of the taxa you are most interested in
  5. Get over the need to have names that are as specific as you want.

We tend to focus on #5 with a dash of #1 and #2. :slight_smile: