#
#     Copyright (C) 1999-2004  Liz Potterton, Peter Briggs
#
#     This code is distributed under the terms and conditions of the
#     CCP4 Program Suite Licence Agreement as a CCP4 Library.
#     A copy of the CCP4 licence can be obtained by writing to the
#     CCP4 Secretary, Daresbury Laboratory, Warrington WA4 4AD, UK.
#
#CCP4i_cvs_Id $Id$
#CCP4I VERSION CCP4Interface 1.3.7
#CCP4I SCRIPT DEF clustalw

TITLE		_title_text		""
INPUT_FILES     _list_of_text           INFILE
OUTPUT_FILES    _list_of_text           OUTFILE

INFILE		_any_file               ""
OUTFILE		_any_file               ""

DIR_INFILE	_default_dirs           ""
DIR_OUTFILE	_default_dirs           ""

OUTPUTTYPE	_clustalw_outputtype	ALN
OUTORDER	_clustalw_outorder	ALIGNED

KTUPLE		_logical		0
KTUPLEN		_int			""

ALIGN		_logical		0
BOOTSTRAP	_logical		0
BOOTSTRAPN	_int			""
QUICKTREE	_logical		0
TYPE		_text			""
EXPTYPE		_clustalw_exptype	""
NEGATIVE	_logical		0

PAIRGAP		_logical		0
PAIRGAPN	_int			""
TOPDIAGS	_logical		0
TOPDIAGSN	_int			""
SCORE		_clustalw_score		PERCENT

PWMATRIX	_logical		0
PWMATRIXN	_clustalw_pwmatrixn	""
PWDNAMATRIX	_logical		0
PWDNAMATRIXN	_clustalw_pwdnamatrixn	""
PWGAPOPEN	_logical		0
PWGAPOPENF	_int			""
PWGAPEXT	_logical		0
PWGAPEXTF	_int			""

MATRIX		_logical		0
MATRIXN		_clustalw_matrixn	""
DNAMATRIX	_logical		0
DNAMATRIXN	_clustalw_dnamatrixn	""
GAPOPEN		_logical		0
GAPOPENF	_int			""
GAPEXT		_logical		0
GAPEXTF		_int			""
ENDGAPS		_logical		0
GAPDIST		_logical		0
GAPDISTN	_int			""
NOPGAP		_logical		0
NOHGAP		_logical		0
HGAPRESIDUES	_logical		0
TRANSWEIGHT	_logical		0
TRANSWEIGHTF	_int			""

PROFILE		_logical		0

SEQUENCES	_logical		0

HELIXGAP	_logical		0
HELIXGAPN	_int			""
STRANDGAP	_logical		0
STRANDGAPN	_int			""
LOOPGAP		_logical		0
LOOPGAPN	_int			""
TERMINALGAP	_logical		0
TERMINALGAPN	_int			""
HELIXENDIN	_logical		0
HELIXENDINN	_int			""
HELIXENDOUT	_logical		0
HELIXENDOUTN	_int			""
STRANDENDIN	_logical		0
STRANDENDINN	_int			""
STRANDENDOUT	_logical		0
STRANDENDOUTN	_int			""

OUTPUTTREE	_logical		0
OUTPUTTREEN	_clustalw_outputtreen	""
SEED		_logical		0
SEEDN		_int			""
KIMURA		_logical		0
TOSSGAPS	_logical		0
BOOTLABELS	_logical		0
BOOTLABELSN	_clustalw_bootlabelsn	""