table of contents
CLUSTALW(1) | Clustal Manual | CLUSTALW(1) |
NAME¶
clustalw - Multiple alignment of nucleic acid and protein sequencesSYNOPSIS¶
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.extInput sequences.
-profile1=file.ext and
-profile2=file.ext
Profiles (old alignment)
VERBS (do things)¶
-optionsList 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.
-ktuple=n
Word size.
-topdiags=n
Number of best diags.
-window=n
Window around best diags.
-pairgap=n
Gap penalty.
-score
PERCENT or ABSOLUTE.
-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.
-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
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.
-sequences
Sequentially add profile2 sequences to profile1
alignment.
-newtree=
File for new guide tree.
-usetree=
File for old guide tree.
-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.
-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 HigginsCopyright 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¶
Copyright © 1988–2010 Des Higgins, Julie Thompson & Toby Giboson (Clustal)NOTES¶
- 1.
- Clustal W and Clustal X version 2.0.
- 2.
- Multiple sequence alignment with the Clustal series of programs.
- 3.
- Multiple sequence alignment with Clustal X
- 4.
- The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.
- 5.
- Using CLUSTAL for multiple sequence alignments.
- 6.
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.
- 7.
- CLUSTAL V: multiple alignment of DNA and protein sequences.
- 8.
- CLUSTAL V: improved software for multiple sequence alignment.
- 9.
- Fast and sensitive multiple sequence alignments on a microcomputer.
- 10.
- CLUSTAL: a package for performing multiple sequence alignment on a microcomputer.
12/28/2010 | Clustal 2.1 |