cd-hit-para(1) [debian man page]
CD-HIT-PARA.PL(1) User Commands CD-HIT-PARA.PL(1) NAME
cd-hit-para.pl - divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs SYNOPSIS
cd-hit-para.pl options DESCRIPTION
This script divide a big clustering job into pieces and submit jobs to remote computers over a network to make it parallel. After all the jobs finished, the script merge the clustering results as if you just run a single cd-hit or cd-hit-est. You can also use it to divide big jobs on a single computer if your computer does not have enough RAM (with -L option). Requirements: 1 When run this script over a network, the directory where you run the scripts and the input files must be available on all the remote hosts with identical path. 2 If you choose "ssh" to submit jobs, you have to have passwordless ssh to any remote host, see ssh manual to know how to set up passwordless ssh. 3 I suggest to use queuing system instead of ssh, I currently support PBS and SGE 4 cd-hit cd-hit-2d cd-hit-est cd-hit-est-2d cd-hit-div cd-hit-div.pl must be in same directory where this script is in. Options -i input filename in fasta format, required -o output filename, required --P program, "cd-hit" or "cd-hit-est", default "cd-hit" --B filename of list of hosts, requred unless -Q or -L option is supplied --L number of cpus on local computer, default 0 when you are not running it over a cluster, you can use this option to divide a big clustering jobs into small pieces, I suggest you just use "--L 1" unless you have enough RAM for each cpu --S Number of segments to split input DB into, default 64 --Q number of jobs to submit to queue queuing system, default 0 by default, the program use ssh mode to submit remote jobs --T type of queuing system, "PBS", "SGE" are supported, default PBS --R restart file, used after a crash of run -h print this help More cd-hit/cd-hit-est options can be speicified in command line Questions, bugs, contact Weizhong Li at liwz@sdsc.edu cd-hit-para.pl 4.6-2012-04-25 April 2012 CD-HIT-PARA.PL(1)
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CD-HIT-2D(1) User Commands CD-HIT-2D(1) NAME
cdhit-2d - quickly group sequences in db1 or db2 format SYNOPSIS
cdhit-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 5, see user's guide for choosing it -l length of throw_away_sequences, default 10 -t tolerance for redundance, default 2 -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 -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 cd-hit-2d 4.6-2012-04-25 April 2012 CD-HIT-2D(1)