CLUSTALW(1)

🎀 NAME 🎀

hey bestie 💖 welcome to clustalw(1), lifted straight out of the Clustal manual and translated into vibes. it's giving "your fave alignment tool has a whole personality."

clustalw — multiple alignment of nucleic acid and protein sequences ✨

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🌈 SYNOPSIS 🌈

okay so the whole thing fits in two little lines, look:

clustalw [-infile] file.ext [OPTIONS]

clustalw [-help | -fullhelp]

that's it. that's the whole entrance. 💅

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🦋 DESCRIPTION 🦋

so Clustal W is a general purpose multiple alignment program for DNA or proteins. no cap. it does the thing where it lines up a whole bunch of sequences at once — nucleotide sequences, amino acid sequences, all of them, simultaneously, together, iconic behaviour. 🔥

the way it's meant to be run is interactively: it gives you a menu and an online help and you just vibe with it. but if you'd rather run it in command-line (batch) mode — very valid, very main character — then you have to hand it several options yourself, and the absolute minimum you can get away with is -infile. periodt. 🫶

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✨ OPTIONS ✨

💾 DATA (sequences)

• -infile=file.ext — the input sequences. your actual data. the moment. 🌸
• -profile1=file.ext and -profile2=file.ext — profiles (old alignment). yes, both of them, together. 💜

🪄 VERBS (do things)

these are the "actually do something" flags, bestie:

• -options — list the command line parameters. 💅
• -help or -check — outline the command line params.
• -fullhelp — output full help content. the deluxe version. ✨
• -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). a thousand little resamples, obsessed. 🎀
• -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). ⚠️ GDE only, don't forget.
• -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. for the introverts. 🤫
• -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. 🌀 (and yes bestie, it is written exactly like that, with no dash — that's not me being sloppy, that's the page.)
• -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.

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💀 BUGS 💀

found a problem? the Clustal bug tracking system lives at

http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal

go tell them, they wanna know. 🙈

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👀 SEE ALSO 👀

clustalx(1). that's the whole list. one (1) friend. 💜

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📚 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.

the academic receipts, all ten of them, we love a citation moment. 🎓✨

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👑 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.

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⚖️ 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. 🫶

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🔗 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

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and that's the whole page, bestie 🎀✨ this lil manual came to you as part of Clustal 2.1, dated 12/28/2010 — yes, a certified vintage icon, and it still ate. go align something pretty. 💖🦋👑