The ClustalW options are summarized in Tables Table 9-1 through Table 9-10.
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.
-infile=file.ext
Input sequences.
-profile1=file.ext
Profiles.
-profile2=file.ext
Profiles (old alignment).
-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).
-ktuple=n
Word size.
-pairgap=n
Gap penalty.
-score
PERCENT or ABSOLUTE.
-topdiags=n
Number of best diags.
-window=n
Window around best diags.
-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.
-dnamatrix=
-endgaps
No end gap separation penalty.
-gapdist=n
Gap separation penalty range.
-gapext=f
-gapopen=f
-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.
-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.
-sequences
Sequentially add profile2 sequences to profile1 alignment.
-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.
-kimura
Use Kimura's correction.
-outputtree=
nj OR phylip OR dist.
-seed=n
Seed number for bootstraps.
-tossgaps
Ignore positions with gaps