9.1 Command-Line Options

The ClustalW options are summarized in Tables Table 9-1 through Table 9-10.

Table 9-1. ClustalW verb options

Option	Definition
-align	Do full multiple alignment.
-bootstrap(=n)	Bootstrap a NJ tree (n= number of bootstraps; def. = 1000).
-convert	Output the input sequences in a different file format.
-help or -check	Outline the command-line parameters
-options	List the command-line parameters.
-tree	Calculate NJ tree.

Table 9-2. ClustalW data options

Option	Definition
-infile=file.ext	Input sequences.
-profile1=file.ext	Profiles.
-profile2=file.ext	Profiles (old alignment).

Table 9-3. ClustalW parameters—general settings

Option	Definition
-case	LOWER or UPPER (for GDE output only).
-interactive	Read command line, then enter normal interactive menus.
-negative	Protein alignment with negative values in matrix.
-outfile=	Sequence alignment file name.
-output=	GCG, GDE, PHYLIP, or PIR.
-outorder=	INPUT or ALIGNED.
-quicktree	Use FAST algorithm for the alignment guide tree.
-seqnos=	OFF or ON (for ClustalW output only).

Table 9-4. ClustalW parameters—fast pairwise alignments

Option	Definition
-ktuple=n	Word size.
-pairgap=n	Gap penalty.
-score	PERCENT or ABSOLUTE.
-topdiags=n	Number of best diags.
-window=n	Window around best diags.

Table 9-5. ClustalW parameters—slow pairwise alignments

Option	Definition
-pwdnamatrix=	DNA weight matrix=IUB, ClustalW, or filename.
-pwgapopen=f	Gap opening penalty.
-pwgapext=f	Gap extension penalty.
-pwmatrix=	Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename.

Table 9-6. ClustalW parameters—multiple alignments

Option	Definition
-dnamatrix=	DNA weight matrix=IUB, ClustalW, or filename.
-endgaps	No end gap separation penalty.
-gapdist=n	Gap separation penalty range.
-gapext=f	Gap extension penalty.
-gapopen=f	Gap opening penalty.
-hgapresidues=	List hydrophilic residue.
-matrix=	Protein weight matrix=BLOSUM, PAM, GONNET, ID, or filename.
-maxdiv=n	Percentage identity for delay.
-newtree=	File for new guide tree.
-nohgap	Hydrophilic gaps off.
-nopgap	Residue-specific gaps off.
-transweight	Transitions weighted.
-type=	PROTEIN or DNA.
-usetree=	File for old guide tree.

Table 9-7. ClustalW parameters—profile alignments

Option	Definition
-newtree1=	File for new guide tree for profile1.
-newtree2=	File for new guide tree for profile2.
-profile	Merge two alignments by profile alignment.
-usetree1=	File for old guide tree for profile1.
-usetree2=	File for old guide tree for profile2.

Table 9-8. ClustalW parameters—sequence to profile alignments

Option	Definition
-newtree=	File for new guide tree.
-sequences	Sequentially add profile2 sequences to profile1 alignment.
-usetree=	File for old guide tree.

Table 9-9. ClustalW parameters—structure alignments

Option	Definition
-helixendin=n	Number of residues inside helix to be treated as terminal.
-helixgap=n	Gap penalty for helix core residues.
-helixendout=n	Number of residues outside helix to be treated as terminal.
-loopgap=n	Gap penalty for loop regions.
-nosecstr1	Do not use secondary structure-gap penalty mask for profile 1.
-nosecstr2	Do not use secondary structure-gap penalty mask for profile 2.
-secstrout=	STRUCTURE or MASK or BOTH or NONE output in alignment file.
-strandgap=n	Gap penalty for strand core residues.
-strandendin=n	Number of residues inside strand to be treated as terminal.
-strandendout=n	Number of residues outside strand to be treated as terminal.
-terminalgap=n	Gap penalty for structure termini.

Table 9-10. ClustalW parameters—trees

Option	Definition
-kimura	Use Kimura's correction.
-outputtree=	nj OR phylip OR dist.
-seed=n	Seed number for bootstraps.
-tossgaps	Ignore positions with gaps