CD-HIT Suite: a web server for clustering and comparing biological sequences

Bioinformatics. 2010 Mar 1;26(5):680-2. doi: 10.1093/bioinformatics/btq003. Epub 2010 Jan 6.


CD-HIT is a widely used program for clustering and comparing large biological sequence datasets. In order to further assist the CD-HIT users, we significantly improved this program with more functions and better accuracy, scalability and flexibility. Most importantly, we developed a new web server, CD-HIT Suite, for clustering a user-uploaded sequence dataset or comparing it to another dataset at different identity levels. Users can now interactively explore the clusters within web browsers. We also provide downloadable clusters for several public databases (NCBI NR, Swissprot and PDB) at different identity levels.

Availability: Free access at

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Cluster Analysis
  • Computational Biology / methods
  • Databases, Genetic
  • Internet
  • Sequence Alignment
  • Sequence Analysis*
  • Software*
  • User-Computer Interface