Taxonomy predictions are written to the
utaxout file. Predictions in the -utaxout
file are written twice: once with confidence values and
once after applying a confidence threshold, keeping only ranks with high enough
confidence. The threshold is
specified by the -utax_cutoff option (default 0.9).
The -rdpout option species an output file in the format
used by the RDP Naive Bayesian Classifier stand-alone program. This is for
compatibility with existing scripts designed for RDP (supported in usearch
v8.1.1786 and later).
The -alnout option specifies a human-readable output file
showing the alignment to the top hit and identities with the nearest neighbors
at each rank (see example file here). This is useful
for manual review of predictions. Note that this option will cause the utax
command to execute more slowly as more calculations are needed to create the
The -fastaout option specifies a FASTA file. Output sequences
are written with a tax= annotation in the labels specifying the taxonomy
prediction with confidences.