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