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 uses a 'longest sequence first' list removal algorithm to remove sequences above a certain identity threshold. Additionally the algorithm implements a very fast heuristic to find high identity segments between sequences, and so can avoid many costly full alignments.
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