clustalw(1)

Usage

clustalw [-infile] file.ext [OPTIONS]

clustalw [{-help | -fullhelp}]

Overview

Clustal W is a general purpose multiple alignment program for DNA or proteins.

The program performs simultaneous alignment of many nucleotide or amino acid sequences. It is typically run interactively, providing a menu and an online help. If you prefer to use it in command-line (batch) mode, you will have to give several options, the minimum being -infile.

Options

DATA (sequences)

-infile=file.ext: Input sequences.

-profile1=file.ext and -profile2=file.ext

Profiles (old alignment)

VERBS (do things)

-options: List the command line parameters.

-help or -check: Outline the command line params.

-fullhelp: Output full help content.

-align: Do full multiple alignment.

-tree: Calculate NJ tree.

-pim: Output percent identity matrix (while calculating the tree).

-bootstrap=n: Bootstrap a NJ tree (n= number of bootstraps; def. = 1000).

-convert: Output the input sequences in a different file format.

PARAMETERS (set things)

General settings:

-interactive: Read command line, then enter normal interactive menus.

-quicktree: Use FAST algorithm for the alignment guide tree.

-type=

PROTEIN or DNA sequences.

-negative: Protein alignment with negative values in matrix.

-outfile=

Sequence alignment file name.

-output=

GCG, GDE, PHYLIP, PIR or NEXUS.

-outputorder=

INPUT or ALIGNED

-case: LOWER or UPPER (for GDE output only).

-seqnos=

OFF or ON (for Clustal output only).

-seqnos_range=

OFF or ON (NEW: for all output formats).

-range=m,n: Sequence range to write starting m to m+n.

-maxseqlen=n: Maximum allowed input sequence length.

-quiet: Reduce console output to minimum.

-stats=file: Log some alignments statistics to file.

Fast Pairwise Alignments:

-ktuple=n: Word size.

-topdiags=n: Number of best diags.

-window=n: Window around best diags.

-pairgap=n: Gap penalty.

-score: PERCENT or ABSOLUTE.

Slow Pairwise Alignments:

-pwmatrix=

:Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename

-pwdnamatrix=

DNA weight matrix=BLOSUMIUB, BLOSUMCLUSTALW or BLOSUMfilename.

-pwgapopen=f: Gap opening penalty.

-pwgapext=f: Gap extension penalty.

Multiple Alignments:

-newtree=

File for new guide tree.

-usetree=

File for old guide tree.

-matrix=

Protein weight matrix=BLOSUM, PAM, GONNET, ID or filename.

-dnamatrix=

DNA weight matrix=IUB, CLUSTALW or filename.

-gapopen=f: Gap opening penalty.

-gapext=f: Gap extension penalty.

-engaps: No end gap separation pen.

-gapdist=n: Gap separation pen. range.

-nogap: Residue-specific gaps off.

-nohgap: Hydrophilic gaps off.

-hgapresidues=

List hydrophilic res.

-maxdiv=n: Percent identity for delay.

-type=

PROTEIN or DNA

-transweight=f: Transitions weighting.

-iteration=

NONE or TREE or ALIGNMENT.

-numiter=n: Maximum number of iterations to perform.

Profile Alignments:

-profile: Merge two alignments by profile alignment.

-newtree1=

File for new guide tree for profile1.

-newtree2=

File for new guide tree for profile2.

-usetree1=

File for old guide tree for profile1.

-usetree2=

File for old guide tree for profile2.

Sequence to Profile Alignments:

-sequences: Sequentially add profile2 sequences to profile1 alignment.

-newtree=

File for new guide tree.

-usetree=

File for old guide tree.

Structure Alignments:

-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.

-helixgap=n: Gap penalty for helix core residues.

-strandgap=n: Gap penalty for strand core residues.

loopgap=n

Gap penalty for loop regions.

-terminalgap=n: Gap penalty for structure termini.

-helixendin=n: Number of residues inside helix to be treated as terminal.

-helixendout=n: Number of residues outside helix to be treated as terminal.

-strandendin=n: Number of residues inside strand to be treated as terminal.

-strandendout=n: Number of residues outside strand to be treated as terminal.

Trees:

-outputtree=nj OR phylip OR dist OR nexus

-seed=n: Seed number for bootstraps.

-kimura: Use Kimura's correction.

-tossgaps: Ignore positions with gaps.

-bootlabels=node: Position of bootstrap values in tree display.

-clustering=

NJ or UPGMA.

References

• Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. (2007). Clustal W and Clustal X version 2.0.[1] Bioinformatics, 23, 2947-2948.

• Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. (2003). Multiple sequence alignment with the Clustal series of programs.[2] Nucleic Acids Res., 31, 3497-3500.

• Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. (1998). Multiple sequence alignment with Clustal X[3]. Trends Biochem Sci., 23, 403-405.

• Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. (1997). The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.[4] Nucleic Acids Res., 25, 4876-4882.

• Higgins DG, Thompson JD, Gibson TJ. (1996). Using CLUSTAL for multiple sequence alignments.[5] Methods Enzymol., 266, 383-402.

• Thompson JD, Higgins DG, Gibson TJ. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.[6] Nucleic Acids Res., 22, 4673-4680.

• Higgins DG. (1994). CLUSTAL V: multiple alignment of DNA and protein sequences.[7] Methods Mol Biol., 25, 307-318

• Higgins DG, Bleasby AJ, Fuchs R. (1992). CLUSTAL V: improved software for multiple sequence alignment.[8] Comput. Appl. Biosci., 8, 189-191.

• Higgins,D.G. and Sharp,P.M. (1989). Fast and sensitive multiple sequence alignments on a microcomputer.[9] Comput. Appl. Biosci., 5, 151-153.

• Higgins,D.G. and Sharp,P.M. (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.[10] Gene, 73, 237-244.

Notes

1.: Clustal W and Clustal X version 2.0.

http://www.ncbi.nlm.nih.gov/pubmed/17846036

2.: Multiple sequence alignment with the Clustal series of programs.

http://www.ncbi.nlm.nih.gov/pubmed/12824352

3.: Multiple sequence alignment with Clustal X

http://www.ncbi.nlm.nih.gov/pubmed/9810230

4.: The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.

http://www.ncbi.nlm.nih.gov/pubmed/9396791

5.: Using CLUSTAL for multiple sequence alignments.

http://www.ncbi.nlm.nih.gov/pubmed/8743695

6.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

http://www.ncbi.nlm.nih.gov/pubmed/7984417

7.: CLUSTAL V: multiple alignment of DNA and protein sequences.

http://www.ncbi.nlm.nih.gov/pubmed/8004173

8.: CLUSTAL V: improved software for multiple sequence alignment.

http://www.ncbi.nlm.nih.gov/pubmed/1591615

9.: Fast and sensitive multiple sequence alignments on a microcomputer.

http://www.ncbi.nlm.nih.gov/pubmed/2720464

10.: CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.

http://www.ncbi.nlm.nih.gov/pubmed/3243435

Releases

Unchanged in 7 releases since Debian 7 (Wheezy).

7–13

Referred to by

neobio(1) Pairwise Amino acid sequence and nucleotide sequence alignment in Java muscle3(1) Multiple Protein Sequence Alignment seaview(1) a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. t_coffee(1) multiple sequence alignment predictprotein(1) analyse protein sequence