NAME

       gthconsensus - build consensus spliced alignments

SYNOPSIS

       gthconsensus [option ...] [file ...]

DESCRIPTION

       Show GenomeThreader output files containing intermediate results and assemble the
       contained spliced alignments to consensus spliced alignments.

OPTIONS

       -translationtable
           set the codon translation table used for codon translation in matching, DP, and output
           default: 1

       -v
           be verbose default: no

       -xmlout
           show output in XML format default: no

       -gff3out
           show output in GFF3 format default: no

       -md5ids
           show MD5 fingerprints as sequence IDs default: no

       -o
           redirect output to specified file default: undefined

       -gzip
           write gzip compressed output file default: no

       -bzip2
           write bzip2 compressed output file default: no

       -force
           force writing to output file default: no

       -gs2out
           output in old GeneSeqer2 format 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

       -intermediate
           stop after calculation of spliced alignments and output results in reusable XML
           format. Do not process this output yourself, use the ``normal'' XML output instead!
           default: no

       -help
           display help for basic options and exit

       -help+
           display help for all options and exit

       -version
           display version information and exit

                                                                                  GTHCONSENSUS(1)