.TH BLASTCLUST 1 2004-06-25 NCBI "NCBI Tools User's Manual"
.SH NAME
blastclust \- BLAST score-based single-linkage clustering
.SH SYNOPSIS
.B blastclust
[\|\fB\-\fP\|]
[\|\fB\-C\fP\|]
[\|\fB\-L\fP\ \fIX\fP\|]
[\|\fB\-S\fP\ \fIX\fP\|]
[\|\fB\-W\fP\ \fIN\fP\|]
[\|\fB\-a\fP\ \fIN\fP\|]
[\|\fB\-b\ F\fP\|]
[\|\fB\-c\fP\ \fIfilename\fP\|]
[\|\fB\-d\fP\ \fIfilename\fP\|]
[\|\fB\-e\ F\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-l\fP\ \fIfilename\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\ F\fP\|]
[\|\fB\-r\fP\ \fIfilename\fP\|]
[\|\fB\-s\fP\ \fIfilename\fP\|]
[\|\fB\-v\fP\ [\|\fIfilename\fP\|]\|]
.SH DESCRIPTION
.PP
\fBblastclust\fP 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. \fBblastclust\fP finds pairs of sequences that have
statistically significant matches and clusters them using
single-linkage clustering.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-C\fP
Complete unfinished clustering
.TP
\fB\-L\fP\ \fIX\fP
Length coverage threshold (default = 0.9)
.TP
\fB\-S\fP\ \fIX\fP
Score coverage threshold (bit score / length if < 3.0, percentage of
identities otherwise; default = 1.75)
.TP
\fB\-W\fP\ \fIN\fP
Use words of size \fIN\fP (length of best perfect match; zero invokes
default behavior: 3 for proteins, 32 for nucleotides)
.TP
\fB\-a\fP\ \fIN\fP
Number of CPU's to use (default = 1)
.TP
\fB\-b\ F\fP
Do not require coverage on both neighbours
.TP
\fB\-c\fP\ \fIfilename\fP
Read advanced options from configuration file \fIfilename\fP
.TP
\fB\-d\fP\ \fIfilename\fP
Input as a database
.TP
\fB\-e\ F\fP
Disable id parsing in database formatting
.TP
\fB\-i\fP\ \fIfilename\fP
FASTA input file (program will format the database and remove files in
the end; default = stdin)
.TP
\fB\-l\fP\ \fIfilename\fP
Restrict reclustering to id list in \fIfilename\fP
.TP
\fB\-o\fP\ \fIfilename\fP
Output file for list of clusters (default = stdout)
.TP
\fB\-p\ F\fP
Input is nucleotides, not proteins.
.TP
\fB\-r\fP\ \fIfilename\fP
Restore neighbors for reclustering from \fIfilename\fP
.TP
\fB\-s\fP\ \fIfilename\fP
Save all neighbours to \fIfilename\fP
.TP
\fB\-v\fP\ [\|\fIfilename\fP\|]
Print verbose progress messages (to \fIfilename\fP)
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.ad l
.BR blast (1),
.BR formatdb (1),
/usr/share/doc/blast2/blastclust.html,
<http://www.ncbi.nlm.nih.gov/BLAST/>