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blastclust - BLAST score-based single-linkage clustering


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]]


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.


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)

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