classify.seqs using the "" as a reference file


I found a problem using the “” as a reference file.

For a sequence EU679419_S001240760 in the reference file,

“” gives “Bacteria;Chloroflexi;Dehalococcoidetes;Dehalogenimonas;”
but the older version, “” gives “Bacteria;“Chloroflexi”;“Dehalococcoidetes”;“Dehalococcoidetes”_order_incertae_sedis;“Dehalococcoidetes”_family_incertae_sedis;Dehalogenimonas;”

For a sequence in my data,
The former result in:
0.2.16 Chloroflexi Dehalococcoidetes Dehalogenimonas unclassified unclassified

The latter result in:
0.2.9 Chloroflexi Dehalococcoidetes Dehalococcoidetes_order_incertae_sedis Dehalococcoidetes_family_incertae_sedis Dehalogenimonas

That is, if I use “”, the sequence is not classified at the genus level.
It seems that many sequences in the “” have the same problem.

Thank you for your concern.


If you have a problem with the RDP reference taxonomy, I would encourage you to bring it up with the RDP. We do very little to change the taxonomy. I would add that as time passes the community gets more information and taxonomic information changes so you should expect things like this to change.


Thank you for your kind reply, Dr. Pschloss,
I got it.