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GT(1) GenomeTools Manual GT(1)

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 (default: no)
-test [yes|no]
perform unit tests and exit (default: no)
-seed [value]
set seed for random number generator manually 0 generates a seed from current time and process id (default: 27016652)
-help
display help and exit
-version
display version information and exit
Tools:
•bed_to_gff3
•cds
•chain2dim
•chseqids
•clean
•compreads
•condenser
•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
•interfeat
•loccheck
•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
•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>.
09/05/2014 GenomeTools 1.5.3