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GT-MATCHTOOL(1) GenomeTools Manual GT-MATCHTOOL(1)

NAME

gt-matchtool - Parse match formats and/or invoke matching tools.

SYNOPSIS

gt matchtool [option ...]

DESCRIPTION

-type [...]
choose match file format: OPENMATCH: open match format, e.g. vmatch BLASTOUT : tabular BLAST output (-m 8) BLASTALLP: invoke BLASTALL with blastp BLASTALLN: invoke BLASTALL with blastn BLASTP : invoke blastp BLASTN : invoke blastn LAST : invoke LAST SW : use Smith-Waterman (default: OPENMATCH)
-matchfile [filename]
set input file name (default: undefined)
-db [filename]
set database file name (default: undefined)
-swminlen [value]
set minimum required alignment length (for Smith-Waterman alignment) (default: 10)
-swmaxedist [value]
set maximum allowed edit distance (for Smith-Waterman alignment) (default: 0)
-query [filename]
set query file name (default: undefined)
-help
display help and exit
-version
display version information and exit

REPORTING BUGS

Report bugs to <gt-users@genometools.org>.
07/29/2016 GenomeTools 1.5.9