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

cd-hit-2d 4.6.4                                   January 2016                                      CD-HIT-2D(1)