NAME

       cd-hit-454 - quickly group sequences, optimised for 454 data

SYNOPSIS

       cdhit-454 [Options]

DESCRIPTION

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

       Options

       -i     input filename in fasta format, required

       -o     output filename, required

       -c     sequence  identity  threshold,  default  0.98  this is a "global sequence identity"
              calculated as : number of identical amino acids in alignment divided  by  the  full
              length of the shorter sequence + gaps

       -b     band_width of alignment, default 10

       -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

       -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

       -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

       -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

       -D     max size per indel, default 1

       -match matching score, default 2

       -mismatch
              mismatching score, default -1

       -gap gap opening score, default -3

       -gap-ext
              gap extension score, default -1

       -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  "Beifang  Niu,  Limin  Fu, Shulei Sun and Weizhong Li. Artificial and
              natural duplicates in pyrosequencing reads of metagenomic data. BMC  Bioinformatics
              (2010) 11:187