xenial (1) blastclust.1.gz

Provided by: blast2_2.2.26.20120620-10_amd64 bug

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/>