Regular Downloads

Lastest CD-HIT-OTU can be downloaded from CD-HIT package, which is hosted at Google Code.

The latest version of CD-HIT-OTU with examples can also be downloaded from here:

software packagesize
cd-hit-otu for 454 reads4.4MB
cd-hit-otu for illumina reads (single or pair end)145MB

More 454 examples
data namesizereference
DivergentGSFLX (with reference)1.7MB[1]
ArtificialGSFLX (with reference)1.3MB[1]
Titanium (with reference and primer)3.6MB[2]
Even and Uneven (with reference)5.2MB[2]
Human gut (real data)7.1MB[3]
Human body (real data)29MB[4]

More Illumina examples (single and pair end)
data name(forward end)data name (reverse end)referencesizereference
E. Coli-1E. Coli-2NA127MB/130MB[5]
19 Strains-119 Strains-2NA306MB/319MB[5]


1. Quince C, Lanzen A, Curtis TP, et al. Accurate determination of microbial diversity from 454 pyrosequencing data.Nat Methods 2009;6:639-41.
2. Quince C, Lanzen A, Davenport RJ, et al. Removing noise from pyrosequenced amplicons. BMC Bioinformatics 2011;12:38.
3. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature 2009;457:U480-7.
4. Costello EK, Lauber CL, Hamady M, et al. Bacterial community variation in human body habitats across space and time. Science 2009;326:1694-7.
5. Degnan PH and Ochman H. Illumina-based analysis of microbial community diversity. Isme Journal 2012;6(1):183-194.
6. Caporaso JG, Lauber CL, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences of the United States of America 2011;108:4516-4522
7. Bartram, AK, Lynch MDJ, et al. Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads (vol 77, pg 3846, 2011). Applied and Environmental Microbiology 2011;77(15):5569-5569.