Who is using CD-HIT

CD-HIT has a very big user base, with tens of thousands of users, and it has been constantly growing. As a general, flexible and powerful clustering method, CD-HIT has been used in many areas. such as: Applicatioins can be found from the papers that cited CD-HIT (external links to Google Scholar):

Li et al (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.
Li et al (2001) Clustering of highly homologous sequences to reduce the size of large protein database.
Li et al (2002) Tolerating some redundancy significantly speeds up clustering of large protein databases.
Huang et al (2010) CD-HIT Suite: a web server for clustering and comparing biological sequences.
Niu et al (2009) Artificial and natural duplicates in pyrosequencing reads of metagenomic data

Indirect impact

CD-HIT has also been indirectly serving more boarder communities by supporting many other resources that use CD-HIT, for example: