NAME

       gt - The GenomeTools genome analysis system.

SYNOPSIS

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

DESCRIPTION

       -i [yes|no]
           enter interactive mode after executing tool or script

       -q [yes|no]
           suppress warnings

       -test [yes|no]
           perform unit tests and exit

       -seed [value]
           set seed for random number generator manually. 0 generates a seed from current time
           and process id

       -help
           display help and exit

       -version
           display version information and exit

       Tools:

       •   bed_to_gff3

       •   cds

       •   chain2dim

       •   chseqids

       •   clean

       •   compreads

       •   condenseq

       •   congruence

       •   convertseq

       •   csa

       •   dot

       •   dupfeat

       •   encseq

       •   encseq2spm

       •   eval

       •   extractfeat

       •   extractseq

       •   fastq_sample

       •   featureindex

       •   fingerprint

       •   genomediff

       •   gff3

       •   gff3_to_gtf

       •   gff3validator

       •   gtf_to_gff3

       •   hop

       •   id_to_md5

       •   inlineseq_add

       •   inlineseq_split

       •   interfeat

       •   loccheck

       •   ltrclustering

       •   ltrdigest

       •   ltrharvest

       •   matchtool

       •   matstat

       •   md5_to_id

       •   merge

       •   mergefeat

       •   mgth

       •   mkfeatureindex

       •   mkfmindex

       •   mmapandread

       •   orffinder

       •   packedindex

       •   prebwt

       •   readjoiner

       •   repfind

       •   scriptfilter

       •   seed_extend

       •   select

       •   seq

       •   seqfilter

       •   seqids

       •   seqmutate

       •   seqorder

       •   seqstat

       •   seqtransform

       •   seqtranslate

       •   sequniq

       •   shredder

       •   shulengthdist

       •   simreads

       •   sketch

       •   sketch_page

       •   snpper

       •   speck

       •   splicesiteinfo

       •   splitfasta

       •   stat

       •   suffixerator

       •   tagerator

       •   tallymer

       •   tirvish

       •   uniq

       •   uniquesub

       •   wtree

       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.

       Set the environment variable GT_SEED to an integer value to supply a seed for the random
       number generator. Can be overridden by the -seed option.

       Combinations are possible. Running the gt binary with GT_ENV_OPTIONS=-help shows all
       possible "environment options".

REPORTING BUGS

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