Usage: gt [option ...] [tool | script] [argument ...] The GenomeTools (gt) genome analysis system (http://genometools.org). -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 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 after 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'') Report bugs to .