Hi @SoilRotifer,
Once again, thanks for the clarification.
In reference to these:
As for the upper-level taxonomy being propagated downward… this is intended by me........When a particular rank is missing, in this case the family level, the taxonomic rank above is propagated downward to a lower rank position until it finds a rank at a lower level, then it propagates that rank downwards towards, and so on… to the genus or species level.
is
d__Bacteria;p__Firmicutes;c__Clostridia; o__Clostridia_UCG-014;f__Clostridia_UCG-014;g__Clostridia_UCG-014
equivalent to
d__Bacteria;p__Firmicutes;c__Clostridia; o__Clostridia_UCG-014;f__;g__
This particular sequence is classified as d__Bacteria;p__Firmicutes;c__Clostridia; o__Clostridia_UCG-014;f__Clostridia_UCG-014;g__Clostridia_UCG-014;__
I guess the reference sequences do not have annotations beyond o__ rank.
Can you help me clarify this?