Provided by: cd-hit_4.6.4-1_amd64 
NAME
cdhit-2d - quickly group sequences in db1 or db2 format
SYNOPSIS
cdhit-2d [Options]
DESCRIPTION
====== CD-HIT version 4.6 (built on Jan 23 2016) ======
Options
-i input filename for db1 in fasta format, required
-i2 input filename for db2 in fasta format, required
-o output filename, required
-c sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity"
calculated as: number of identical amino acids in alignment divided by the full length of the
shorter sequence
-G use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated
as : number of identical amino acids in alignment divided by the length of the alignment NOTE!!!
don't use -G 0 unless you use alignment coverage controls see options -aL, -AL, -aS, -AS
-b band_width of alignment, default 20
-M memory limit (in MB) for the program, default 800; 0 for unlimitted;
-T number of threads, default 1; with 0, all CPUs will be used
-n word_length, default 5, see user's guide for choosing it
-l length of throw_away_sequences, default 10
-t tolerance for redundance, default 2
-d length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops
at first space
-s length difference cutoff, default 0.0 if set to 0.9, the shorter sequences need to be at least 90%
length of the representative of the cluster
-S length difference cutoff in amino acid, default 999999 if set to 60, the length difference between
the shorter sequences and the representative of the cluster can not be bigger than 60
-s2 length difference cutoff for db1, default 1.0 by default, seqs in db1 >= seqs in db2 in a same
cluster if set to 0.9, seqs in db1 may just >= 90% seqs in db2
-S2 length difference cutoff, default 0 by default, seqs in db1 >= seqs in db2 in a same cluster if
set to 60, seqs in db2 may 60aa longer than seqs in db1
-aL alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers
90% of the sequence
-AL alignment coverage control for the longer sequence, default 99999999 if set to 60, and the length
of the sequence is 400, then the alignment must be >= 340 (400-60) residues
-aS alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers
90% of the sequence
-AS alignment coverage control for the shorter sequence, default 99999999 if set to 60, and the length
of the sequence is 400, then the alignment must be >= 340 (400-60) residues
-A minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this
value for both sequences
-uL maximum unmatched percentage for the longer sequence, default 1.0 if set to 0.1, the unmatched
region (excluding leading and tailing gaps) must not be more than 10% of the sequence
-uS maximum unmatched percentage for the shorter sequence, default 1.0 if set to 0.1, the unmatched
region (excluding leading and tailing gaps) must not be more than 10% of the sequence
-U maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading
and tailing gaps) must not be more than 10 bases
-B 1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on
hard drive it is recommended to use -B 1 for huge databases
-p 1 or 0, default 0 if set to 1, print alignment overlap in .clstr file
-g 1 or 0, default 0 by cd-hit's default algorithm, a sequence is clustered to the first cluster that
meet the threshold (fast cluster). If set to 1, the program will cluster it into the most similar
cluster that meet the threshold (accurate but slow mode) but either 1 or 0 won't change the
representatives of final clusters
-bak write backup cluster file (1 or 0, default 0)
-h print this help
Questions, bugs, contact Weizhong Li at liwz@sdsc.edu
If you find cd-hit useful, please kindly cite:
"Clustering of highly homologous sequences to reduce thesize of large protein database", Weizhong
Li, Lukasz Jaroszewski & Adam Godzik. Bioinformatics, (2001) 17:282-283 "Cd-hit: a fast program
for clustering and comparing large sets of protein or nucleotide sequences", Weizhong Li & Adam
Godzik. Bioinformatics, (2006) 22:1658-1659