~~和唐老师一个实验室的人开发的~~
CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CD-HIT was originally developed by Dr. Weizhong Liat Dr. Adam Godzik‘s Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)
CD-HIT is very fast and can handle extremely large databases. CD-HIT helps to significantly reduce the computational and manual efforts in many sequence analysis tasks and aids in understanding the data structure and correct the bias within a dataset.
The CD-HIT package has CD-HIT, CD-HIT-2D, CD-HIT-EST, CD-HIT-EST-2D, CD-HIT-454, CD-HIT-PARA, PSI-CD-HIT, CD-HIT-OTU, CD-HIT-LAP, CD-HIT-DUP and over a dozen scripts.
- CD-HIT (CD-HIT-EST) clusters similar proteins (DNAs) into clusters that meet a user-defined similarity threshold.
- CD-HIT-2D (CD-HIT-EST-2D) compares 2 datasets and identifies the sequences in db2 that are similar to db1 above a threshold.
- CD-HIT-454 identifies natural and artificial duplicates from pyrosequencing reads.
- CD-HIT-OTU clusters rRNA tags into OTUs
- CD-HIT-DUP identifies duplicates from single or paired Illumina reads
- CD-HIT-LAP identifies overlapping reads
The usage of other programs and scripts can be found in CD-HIT user‘s guide.
CD-HIT is currently maintained by the Dr. Li‘s group (http://weizhongli-lab.org/) at J Craig Venter Institute. We thank the support from National Center for Research Resources (Grant # 1R01RR025030, 2008-2011). We thank all users that report bugs, give us suggestions and comments.
下载：
https://github.com/weizhongli/cdhit/releases
解压
安装： sudo make
freemao
FAFU