man blastclust (Commandes) - BLAST score-based single-linkage clustering
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.