NAME

       cd-hit - quickly group sequences

SYNOPSIS

       cd-hit [Options]

DESCRIPTION

              ====== CD-HIT version 4.8.1 (built on Mar 22 2020) ======

       Options

       -i     input filename in fasta format, required, can be in .gz format

       -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  or  bases  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  or  bases  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

       -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 !! No longer supported !!

       -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

       -sc    sort clusters by  size  (number  of  sequences),  default  0,  output  clusters  by
              decreasing length if set to 1, output clusters by decreasing size

       -sf    sort  fasta/fastq  by  cluster size (number of sequences), default 0, no sorting if
              set to 1, output sequences by decreasing cluster size this can be very slow if  the
              input is in .gz format

       -bak write backup cluster file (1 or 0, default 0)

       -h     print this help

              Questions,  bugs,  contact  Weizhong  Li  at liwz@sdsc.edu For updated versions and
              information, please visit: http://cd-hit.org

              or https://github.com/weizhongli/cdhit

              cd-hit web server is also available from http://cd-hit.org

              If you find cd-hit useful, please kindly cite:

              "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 "CD-HIT: accelerated for clustering  the  next  generation  sequencing
              data", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu & Weizhong Li. Bioinformatics,
              (2012) 28:3150-3152