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