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# gthgetseq(1)
## NAME
gthgetseq - get FASTA sequences from GenomeThreader files
## SYNOPSIS
*gthgetseq* -getcdna | -getprotein | -getgenomic [option ...] [file ...]
## DESCRIPTION
Get FASTA sequences from GenomeThreader files containing intermediate results.
The sequences are shown on stdout.
## OPTIONS
*-getcdna*::
get cDNA/EST sequences
default: no
*-getcdnacomp*::
get complement of cDNA/EST sequences
default: no
*-getprotein*::
get protein sequences
default: no
*-getproteincomp*::
get complement of protein sequences
default: no
*-getgenomic*::
get genomic sequences
default: no
*-getgenomiccomp*::
get complement of genomic sequences
default: no
*-minalignmentscore*::
set the minimum alignment score for spliced alignments to be
included into the set of spliced alignments
default: 0.00
*-maxalignmentscore*::
set the maximum alignment score for spliced alignments to be
included into the set of spliced alignments
default: 1.00
*-mincoverage*::
set the minimum coverage for spliced alignments to be
included into the set of spliced alignments
default: 0.00
*-maxcoverage*::
set the maximum coverage for spliced alignments to be
included into the set of spliced alignments
default: 9999.99
*-gzip*::
gzip compressed input file(s)
default: no
*-bzip2*::
bzip2 compressed input file(s)
default: no
*-help*::
display help and exit
*-version*::
display version information and exit
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