.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH CD-HIT-454 "1" "June 2017" "cd-hit-454 4.6.7" "User Commands"
.SH NAME
cd-hit-454 \- quickly group sequences, optimised for 454 data
.SH SYNOPSIS
.B cd-hit-454
[\fI\,Options\/\fR]
.SH DESCRIPTION
.IP
====== CD\-HIT version 4.7 (built on Jun 14 2017) ======
.PP
Options
.TP
\fB\-i\fR
input filename in fasta format, required
.TP
\fB\-o\fR
output filename, required
.TP
\fB\-c\fR
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
.TP
\fB\-b\fR
band_width of alignment, default 10
.TP
\fB\-M\fR
memory limit (in MB) for the program, default 800; 0 for unlimitted;
.TP
\fB\-T\fR
number of threads, default 1; with 0, all CPUs will be used
.TP
\fB\-n\fR
word_length, default 10, see user's guide for choosing it
.TP
\fB\-aL\fR
alignment coverage for the longer sequence, default 0.0
if set to 0.9, the alignment must covers 90% of the sequence
.TP
\fB\-AL\fR
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
.TP
\fB\-aS\fR
alignment coverage for the shorter sequence, default 0.0
if set to 0.9, the alignment must covers 90% of the sequence
.TP
\fB\-AS\fR
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
.TP
\fB\-B\fR
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 !!
.TP
\fB\-g\fR
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
.TP
\fB\-D\fR
max size per indel, default 1
.TP
\fB\-match\fR
matching score, default 2
.TP
\fB\-mismatch\fR
mismatching score, default \fB\-1\fR
.HP
\fB\-gap\fR gap opening score, default \fB\-3\fR
.TP
\fB\-gap\-ext\fR
gap extension score, default \fB\-1\fR
.HP
\fB\-bak\fR write backup cluster file (1 or 0, default 0)
.TP
\fB\-h\fR
print this help
.IP
Questions, bugs, contact Weizhong Li at liwz@sdsc.edu
.IP
If you find cd\-hit useful, please kindly cite:
.IP
"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
"Beifang Niu, Limin Fu, Shulei Sun and Weizhong Li. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinformatics (2010) 11:187