--- name: "clustalw" section: "1" platform: "linux" package: "clustalw" version: "2.1+lgpl-7" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/clustalw" --- # clustalw(1) Multiple alignment of nucleic acid and protein sequences ## 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=*BLOSUM*IUB, *BLOSUM*CLUSTALW or *BLOSUM*filename. - **-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)](/clustalx/1.md). ## 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** \ Prepared this manpage in DocBook XML for the Debian distribution. ## COPYRIGHT 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