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       blastclust - BLAST score-based single-linkage clustering


       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]]


       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.


       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)


       The National Center for Biotechnology Information.


       blast(1), formatdb(1), /usr/share/doc/blast2/blastclust.html,