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


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


gt matchtool [option ...]


-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)


display help and exit


display version information and exit


Report bugs to

11/28/2022 GenomeTools 1.6.2