GT(1)

NAME
gt - The GenomeTools (gt) genome analysis system (http://genometools.org).

SYNOPSIS

gt [option ...] [tool | script] [argument ...]

OPTIONS

-i
    enter interactive mode after executing tool or script

-test
    perform unit tests and exit

-help
    display help and exit

-version
    display version information and exit

DESCRIPTION

Tools:

bed_to_gff3 cds chain2dim chseqids clean compreads congruence convertseq csa dupfeat encseq encseq2spm eval extractfeat extractseq featureindex fingerprint genomediff gff3 gff3_to_gtf gff3validator gtf_to_gff3 hop id_to_md5 interfeat ltrclustering ltrdigest ltrharvest matchtool matstat md5_to_id merge mergefeat mgth mkfeatureindex mkfmindex mmapandread orffinder packedindex prebwt readjoiner repfind scriptfilter select seq seqfilter seqids seqmutate seqorder seqstat seqtransform seqtranslate sequniq shredder shulengthdist simreads sketch sketch_page splicesiteinfo splitfasta stat suffixerator tagerator tallymer uniq uniquesub

Set the environment variable GT_MEM_BOOKKEEPING=on to enable memory bookkeeping (e.g., like this: env GT_MEM_BOOKKEEPING=on gt).

Set the environment variable GT_ENV_OPTIONS=-spacepeak to show a spacepeak afte r program run. Set the environment variable GT_ENV_OPTIONS=-showtime to show processing times for some program parts if implemented.

Combinations are possible. Running the ‘gt’ binary with GT_ENV_OPTIONS=-help shows all possible “environment options”)

AUTHOR

Report bugs to <gt-users@genometools.org>.