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blastclust(1) [debian man page]

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

NCBI
								    2004-06-25							     BLASTCLUST(1)

Check Out this Related Man Page

ASN2FSA(1)						     NCBI Tools User's Manual							ASN2FSA(1)

NAME

       asn2fsa - convert biological sequence data from ASN.1 to FASTA

SYNOPSIS

       asn2fsa [-] [-A acc] [-D] [-E] [-H] [-L filename] [-T] [-a type] [-b] [-c] [-d path] [-e N] [-f path] [-g] [-h filename] [-i filename] [-k]
       [-l] [-m] [-o filename] [-p path] [-q filename] [-r] [-s] [-u] [-v filename] [-x str] [-z]

DESCRIPTION

       asn2fsa converts biological sequence data from ASN.1 to FASTA.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -A acc Accession to fetch

       -D     Use Dash for Gap

       -E     Extended Seq-ids

       -H     HTML spans

       -L filename
	      Log file

       -T     Use Threads

       -a type
	      Input ASN.1 type:
	      a      Automatic (default)
	      z      Any
	      e      Seq-entry
	      b      Bioseq
	      s      Bioseq-set
	      m      Seq-submit
	      t      batch processing (suitable for official releases; autodetects specific type)

       -b     Bioseq-set is Binary

       -c     Bioseq-set is Compressed

       -d path
	      Path to ReadDB Database

       -e N   Line length (70 by default; may range from 10 to 120)

       -f path
	      Path to indexed FASTA data

       -g     Expand delta gaps into Ns

       -h filename
	      Far component cache output file name

       -i filename
	      Single input file (standard input by default)

       -k     Local fetching

       -l     Lock components in advance

       -m     Master style for near segmented sequences

       -o filename
	      Nucleotide Output file name

       -p path
	      Path to ASN.1 Files

       -q filename
	      Quality score output file name

       -r     Remote fetching from NCBI

       -s     Far genomic contig for quality scores

       -u     Recurse

       -v filename
	      Protein output file name

       -x str File selection substring (.ent by default) [String]

       -z     Print quality score gap as -1

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asn2all(1), asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1).

NCBI
								    2011-09-02								ASN2FSA(1)
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