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

                                                                                                    GTHGETSEQ(1)