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

NAME

cd-hit-2d - quickly group sequences in db1 or db2 format

SYNOPSIS

cd-hit-2d [Options]

DESCRIPTION

====== CD-HIT version 4.8.1 (built on Nov 21 2020) ======

Options

input filename for db1 in fasta format, required, can be in .gz format
input filename for db2 in fasta format, required, can be in .gz format
output filename, required
sequence identity threshold, default 0.9 this is the default cd-hit's "global sequence identity" calculated as: number of identical amino acids or bases in alignment divided by the full length of the shorter sequence
use global sequence identity, default 1 if set to 0, then use local sequence identity, calculated as : number of identical amino acids or bases 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
band_width of alignment, default 20
memory limit (in MB) for the program, default 800; 0 for unlimitted;
number of threads, default 1; with 0, all CPUs will be used
word_length, default 5, see user's guide for choosing it
length of throw_away_sequences, default 10
tolerance for redundance, default 2
length of description in .clstr file, default 20 if set to 0, it takes the fasta defline and stops at first space
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
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
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
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
alignment coverage for the longer sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
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
alignment coverage for the shorter sequence, default 0.0 if set to 0.9, the alignment must covers 90% of the sequence
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
minimal alignment coverage control for the both sequences, default 0 alignment must cover >= this value for both sequences
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
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
maximum unmatched length, default 99999999 if set to 10, the unmatched region (excluding leading and tailing gaps) must not be more than 10 bases
1 or 0, default 0, by default, sequences are stored in RAM if set to 1, sequence are stored on hard drive !! No longer supported !!
1 or 0, default 0 if set to 1, print alignment overlap in .clstr file
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)

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Questions, bugs, contact Weizhong Li at liwz@sdsc.edu
If you find cd-hit useful, please kindly cite:
"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: accelerated for clustering the next generation sequencing data", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu & Weizhong Li. Bioinformatics, (2012) 28:3150-3152
November 2020 cd-hit-2d 4.8.1