CD-HIT-EST-2D(1)						   User Commands						  CD-HIT-EST-2D(1)

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 Apr 26 2012) ======

       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 tail-
	      ing 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  clus-
	      ter).  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

cd-hit-est-2d 4.6-2012-04-25					    April 2012							  CD-HIT-EST-2D(1)