CD-HIT alignments are gappy

<< CD-HIT analysis
<< Comparing USEARCH and CD-HIT
Below are two alignments of a pair of 16S reads (in FASTA format at bottom of this page). The top alignment is by CD-HIT-EST v4.5.7, which has 13 gapped columns (not including terminal gaps), and gives an identity of 98% according to the CD-HIT definition, which does not count gaps in the longer sequence as differences. The lower alignment is by USEARCH, which has 9 internal gapped columns and gives 95% using CD-HIT's measure of identity (--iddef 0 option). See here for instructions on how to view CD-HIT alignments.

CD-HIT alignments have spurious matches in gappy regions
Many matches in gappy regions in CD-HIT alignments are probably spurious (example in red box below). 

Taxonomic distance
The RDP Naive Bayesian Classifier assigns both reads to order Clostridiales, with tentative assignment to the same family (Ruminococcaceae, with P=0.25 for F12Fcsw_257171 and P=0.48 for M13Fcsw_294419), but different genera. Since the RDP classifier uses an alignment-free method, we can assume that it is independent of alignment biases. In this example, the divergence reported by USEARCH is closer to the expected taxonomic divergence.