# gthconsensus(1)

## 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
