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CD-HIT-EST (version 1.3)
It is suggested to adjust word size in function of similarity threshold. 8,9 or 10 for threshold in [0.9;1.0] interval, 7 for [0.88;0.9], 6 for [0.85;0.88], 5 for [0.80;0.85], 4 for [0.75;0.8] (-n)
In cd-hit's default algorithm, a sequence is clustered to the first cluster that meet the threshold (fast cluster). If set to slow, the program will cluster it into the most similar cluster that meet the threshold (accurate but slow mode). This won't change the representatives of final clusters (-g)

What it does

CD-HIT stands for Cluster Database at High Identity with Tolerance. The program (cd-hit) takes a fasta format sequence database as input and produces a set of 'non-redundant' (nr) representative sequences as output. In addition cd-hit outputs a cluster file, documenting the sequence 'groupies' for each nr sequence representative. The idea is to reduce the overall size of the database without removing any sequence information by only removing 'redundant' (or highly similar) sequences. This is why the resulting database is called non-redundant (nr). Essentially, cd-hit produces a set of closely related protein families from a given fasta sequence database.


cd-hit-est requires a fasta file as input.


The first output is a fasta file containing representative sequences.

The second output is a text file listing the mapping of sequences to the representative sequences:

>Cluster 0
0 2799aa, >PF04998.6|RPOC2_CHLRE/275-3073... *
>Cluster 1
0 2214aa, >PF06317.1|Q6Y625_9VIRU/1-2214... at 80%
1 2215aa, >PF06317.1|O09705_9VIRU/1-2215... at 84%
2 2217aa, >PF06317.1|Q6Y630_9VIRU/1-2217... *
3 2216aa, >PF06317.1|Q6GWS6_9VIRU/1-2216... at 84%
4 527aa, >PF06317.1|Q67E14_9VIRU/6-532... at 63%
>Cluster 2
0 2202aa, >PF06317.1|Q6UY61_9VIRU/8-2209... at 60%
1 2208aa, >PF06317.1|Q6IVU4_JUNIN/1-2208... *
2 2207aa, >PF06317.1|Q6IVU0_MACHU/1-2207... at 73%
3 2208aa, >PF06317.1|RRPO_TACV/1-2208... at 69%