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



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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