Provided by: cd-hit_4.8.1-2build1_amd64 
NAME
cd-hit-est-2d - run CD-HIT algorithm on RNA/DNA sequences in db1 or db2 format
SYNOPSIS
cd-hit-est-2d [Options]
DESCRIPTION
====== CD-HIT version 4.8.1 (built on Mar 22 2020) ======
Options
-i input filename for db1 in fasta format, required, can be in .gz format
-i2 input filename for db2 in fasta format, required, can be in .gz format
-j, -j2
input filename in fasta/fastq format for R2 reads if input are paired end (PE) files
-i db1-R1.fq -j db1-R2.fq -i2 db2-R1.fq -j2 db2-R2.fq -o output_R1 -op output_R2 or
-i db1-R1.fa -j db1-R2.fa -i2 db2-R1.fq -j2 db2-R2.fq -o output_R1 -op output_R2
-o output filename, required
-op output filename for R2 reads if input are paired end (PE) files
-c 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
-G 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
-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 !! No longer supported !!
-P input paired end (PE) reads, default 0, single file if set to 1, please use -i R1 -j R2 to input
both PE files
-cx length to keep after trimming the tail of sequence, default 0, not trimming if set to 50, the
program only uses the first 50 letters of input sequence
-cy length to keep after trimming the tail of R2 sequence, default 0, not trimming if set to 50, the
program only uses the first 50 letters of input R2 sequence e.g. -cx 100 -cy 80 for paired end
reads
-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 Weizhong Li at liwz@sdsc.edu For updated versions and information, please
visit: http://cd-hit.org
or https://github.com/weizhongli/cdhit
cd-hit web server is also available from http://cd-hit.org
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