NAME

       cdhit-est-2d - run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format

SYNOPSIS

       cdhit-est-2d [Options]

DESCRIPTION

              ====== CD-HIT version 4.6 (built on Oct 21 2013) ======

       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 10, see user's guide for choosing it

       -l     length of throw_away_sequences, default 10

       -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

       -r     1 or 0, default 1, by default do both +/+ & +/- alignments if set to  0,  only  +/+
              strand alignment

       -mask  masking letters (e.g. -mask NX, to mask out both 'N' and 'X')

       -match matching score, default 2 (1 for T-U and N-N)

       -mismatch
              mismatching score, default -2

       -gap gap opening score, default -6

       -gap-ext
              gap extension score, default -1

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

       -h     print this help

              Questions, bugs, contact Limin Fu at l2fu@ucsd.edu, or Weizhong Li at liwz@sdsc.edu
              For updated versions and information, please visit: http://cd-hit.org

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

              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