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
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), blastclust.html,
<http://www.ncbi.nlm.nih.gov/BLAST/>
NCBI 2004-06-25 BLASTCLUST(1)
permalink to the blastclust command:
https://manpage.me/?blastclust
link by Name, Section, and OS version of this man page:
/?q=blastclust&sektion=1&manpath=FreeBSD+11.1-RELEASE+and+Ports