PSI-CD-HIT-2D.PL(1)						   User Commands					       PSI-CD-HIT-2D.PL(1)

NAME

       psi-cd-hit-2d.pl - runs similar algorithm like CD-HIT but using BLAST to calculate similarities in db1 or db2 format

DESCRIPTION

       Usage psi-cd-hit-2d [Options]

       Options

       -i     in_dbname, required

       -o     out_dbname, required

       -c     clustering threshold (sequence identity), default 0.3

       -ce clustering threshold (blast expect), default -1,

	      it  means  by default it doesn't use expect threshold, but with positive value, the program cluster seqs if similarities meet either
	      identity threshold or expect threshold

       -L     coverage of shorter sequence ( aligned / full), default 0.0

       -M     coverage of longer sequence ( aligned / full), default 0.0

       -R     (1/0) use psi-blast profile? default 0 perform psi-blast / pdb-blast type search

       -G     (1/0) use global identity? default 1 sequence identity calculated as

	      total identical residues of local alignments / length of shorter seq

	      if you prefer to use -G 0, it is suggested that you also use -L, such as -L 0.8, to prevent very short matches.

       -d     length of description line in the .clstr file, default 30 if set to 0, it takes the fasta defline and stops at first space

       -l     length_of_throw_away_sequences, default 10

       -p     profile search para, default

	      "-a 2 -d nr80 -j 3 -F F -e 0.001 -b 500 -v 500"

       -bfdb profile database, default nr80

       -s     blast search para, default

	      "-F F -e 0.000001 -b 100000 -v 100000"

       -be blast expect cutoff, default 0.000001

       -b     filename of list of hosts to run this program in parallel with ssh calls, you need provide a list of hosts

       -pbs No of jobs to send each time by PBS querying system

	      you can not use both ssh and pbs at same time

       -k (1/0) keep blast raw output file, default 1

       -rs steps of save restart file and clustering output, default 5000

	      everytime after process 5000 sequences, program write a restart file and current clustering information

       -restart restart file, readin a restart file

	      if program crash, stoped, termitated, you can restart it by add a option "-restart sth.restart"

       -rf steps of re format blast database, default 200,000

	      if program clustered 200,000 seqs, it remove them from seq pool, and re format blast db to save time

       -local dir of local blast db,

	      when run in parallel with ssh (not pbs), I can copy blast dbs to local drives on each node to save blast db reading time BUT, IT MAY
	      NOT FASTER

       -J     job, job_file, exe specific jobs like parse blast outonly DON'T use it, it is only used by this program itself

       -single files of ids those you known that they are singletons

	      so I won't run them as queries

       -i2 second input database

       -blastn run blastn, default 0

       -lo how long can seq in db2 > db1 in a cluster, default 0

	      means, that seq in db2 should <= seqs in db1 in a cluster

	      ============================== by Weizhong Li, 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
	      GodzikBioinformatics, (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

psi-cd-hit-2d.pl 4.6-2012-04-25 				    April 2012						       PSI-CD-HIT-2D.PL(1)