How to view CD-HIT alignments

 
<< CD-HIT analysis
<< Comparing USEARCH and CD-HIT
  
How to generate an alignment using CD-HIT
To review the alignment for a given pair, you can re-compile CD-HIT with the MAKEALIGN macro defined. Then run CD-HIT with the lowest permitted cutoff, e.g.:

  cd-hit-est -i pair.fasta -o pair -c 0.8

If the pair has 80% or higher identity according to CD-HIT, the alignment will be written to a file named alignments.txt.

This method applies to CD-HIT v4 at least through version 4.5.7.

How to generate an alignment using USEARCH
USEARCH offers a rich set of options for reviewing alignments and derived values (%id, E-value etc.), including --uc, --blastout, --blast6out, --fastapairs and --userout. CD-HIT provides only the %id of a hit via the .clstr output file.