CD-HIT banding causes more errors than USEARCH banding USEARCH also uses banding by default, but the strategy is quite different, and the --band option of USEARCH isnotequivalent to the -b option of CD-HIT. In CD-HIT, the band spans the entire alignment. In USEARCH banding is used only...
Cd-hit and cd-hit-est clustering For eukaryotic genes, long introns can cause long gaps in sequence alignments, which significantly reduces the efficiency of short word filtering. So, practically, cd-hit-est can be applied only for non-intron-containing sequences, such as ESTs. What is dbEST...