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 sequences 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,  percentage  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), /usr/share/doc/blast2/blastclust.html,
       <http://www.ncbi.nlm.nih.gov/BLAST/>