Provided by: clustalw_2.1+lgpl-7_amd64
clustalw - Multiple alignment of nucleic acid and protein sequences
clustalw [-infile] file.ext [OPTIONS] clustalw [-help | -fullhelp]
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.
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.
The Clustal bug tracking system can be found at http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal.
• 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. 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. Nucleic Acids Res., 31, 3497-3500. • Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ. (1998). Multiple sequence alignment with Clustal X. 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. Nucleic Acids Res., 25, 4876-4882. • Higgins DG, Thompson JD, Gibson TJ. (1996). Using CLUSTAL for multiple sequence alignments. 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. Nucleic Acids Res., 22, 4673-4680. • Higgins DG. (1994). CLUSTAL V: multiple alignment of DNA and protein sequences. Methods Mol Biol., 25, 307-318 • Higgins DG, Bleasby AJ, Fuchs R. (1992). CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci., 8, 189-191. • Higgins,D.G. and Sharp,P.M. (1989). Fast and sensitive multiple sequence alignments on a microcomputer. 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. Gene, 73, 237-244.
Des Higgins Copyright holder for Clustal. Julie Thompson Copyright holder for Clustal. Toby Gibson Copyright holder for Clustal. Charles Plessy <email@example.com> 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.
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