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clustalw - Multiple alignment of nucleic acid and protein sequences

CLUSTALW(1) Clustal Manual CLUSTALW(1)

NAME

clustalw - Multiple alignment of nucleic acid and protein sequences

SYNOPSIS

clustalw [ -infile] file.ext [OPTIONS]
clustalw [ -help | -fullhelp]

DESCRIPTION

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.

BUGS

The Clustal bug tracking system can be found at http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal.

SEE ALSO

clustalx(1).

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.

AUTHORS

Des Higgins
Copyright holder for Clustal.
Julie Thompson
Copyright holder for Clustal.
Toby Gibson
Copyright holder for Clustal.
Charles Plessy <plessy@debian.org>
Prepared this manpage in DocBook XML for the Debian distribution.
Copyright © 1988–2010 Des Higgins, Julie Thompson & Toby Giboson (Clustal)
 
Copyright © 2008–2010 Charles Plessy (This manpage)
 
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public License along with this program. If not, see http://www.gnu.org/licenses/, or on Debian systems, /usr/share/common-licenses/LGPL-3.
This manual page and its XML source can be used, modified, and redistributed as if it were in public domain.
 

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
12/28/2010 Clustal 2.1