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 https://github.com/genometools/genometools/issues.