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BLASTCLUST(1)		   NCBI	Tools User's Manual		 BLASTCLUST(1)

NAME
       blastclust - BLAST score-based single-linkage clustering

SYNOPSIS
       blastclust  [-]	[-C]  [-L X] [-S X] [-W	N] [-a N] [-b F] [-c filename]
       [-d filename] [-e F] [-i	filename] [-l filename]	 [-o filename]	[-p F]
       [-r filename] [-s filename] [-v [filename]]

DESCRIPTION
       blastclust automatically	and systematically clusters protein or DNA se-
       quences based on	pairwise matches found using the  BLAST	 algorithm  in
       case  of	proteins or Mega BLAST algorithm for DNA. In the latter	case a
       single Mega BLAST search	is performed for all  the  sequences  combined
       against	a  database  created from the same sequences. blastclust finds
       pairs of	sequences that	have  statistically  significant  matches  and
       clusters	them using single-linkage clustering.

OPTIONS
       A summary of options is included	below.

       -      Print usage message

       -C     Complete unfinished clustering

       -L X   Length coverage threshold	(default = 0.9)

       -S X   Score  coverage threshold	(bit score / length if < 3.0, percent-
	      age of identities	otherwise; default = 1.75)

       -W N   Use words	of size	N (length of best perfect match; zero  invokes
	      default behavior:	3 for proteins,	32 for nucleotides)

       -a N   Number of	CPU's to use (default =	1)

       -b F   Do not require coverage on both neighbours

       -c filename
	      Read advanced options from configuration file filename

       -d filename
	      Input as a database

       -e F   Disable id parsing in database formatting

       -i filename
	      FASTA  input  file  (program will	format the database and	remove
	      files in the end;	default	= stdin)

       -l filename
	      Restrict reclustering to id list in filename

       -o filename
	      Output file for list of clusters (default	= stdout)

       -p F   Input is nucleotides, not	proteins.

       -r filename
	      Restore neighbors	for reclustering from filename

       -s filename
	      Save all neighbours to filename

       -v [filename]
	      Print verbose progress messages (to filename)

AUTHOR
       The National Center for Biotechnology Information.

SEE ALSO
       blast(1), formatdb(1), blastclust.html,
       <http://www.ncbi.nlm.nih.gov/BLAST/>

NCBI				  2004-06-25			 BLASTCLUST(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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