Clustal W

CLUSTAL W

Program status

The bcf program suite containing clustalw seems to have disappeared.
Version 2.05 is installed in the suite of programs maintained by Dr. Hardies.

Place /home/hardies/apps in your path, and then clustalw2 will run when you type clustalw.

Versions of clustal can be found in many applications and web pages. Often many of the options and capabilities are missing. All versions conduct a progressive alignment, whereby the closest sequences are aligned first. Remote clustal W alignments may be computed with many but not all options at http://www.ebi.ac.uk/clustalw/

Capabilities of ClustalW 2.05 include:

Ability to align sections separately, manually edit them, and then put the sections together.
Ability to do an NJ tree after alignment (a better tree than the cladogram generated during the alignment).

Can output the distance matrix or do bootstrap analysis.

Secondary structure information can be added to a sequence and used to steer gap placement.
User defined position specific gap penalties can be manually added (but not automatically computed).
Some ability to fine tune gap placement parameters.
Input and output in a variety of formats.

Because ClustalW incorporates a Neighbor Joining phylogenetic analysis and and a Bootstrap analysis, it can directly support the first steps of a phylogenetic analysis. Note that for divergent sequences, it is often necessary to reduce noise by confining the analysis to the more conserved blocks of sequence. We expect an implementation of PAUP soon, which has the best facilities for exploring that strategy.

See also clustalW embedded in the SeaView editor, and the in the PC packages Vector NTI, and LaserGene, which are under a site license at UTHSCSA.

The program is run on bioinf by the command clustalw. Upon running the program, a tree structured menu appears to guide the use of the program.

Documentation

Each menu page in the clustalw menu system has context-specific help.
The collection of context-specific help messages for version 2.05.
Thompson, J D; Higgins, D G; Gibson, T J 1994. CLUSTAL W: improving the sensitivity of

version on web without figures

For information about some other flavors of Clustal, see Jeanmougin F. Thompson JD. Gouy M. Higgins DG. Gibson TJ. 1998. Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences. 23(10):403-5, and citations therein.

CLUSTAL format.

Often indicated by .aln extension.
Example:

CLUSTAL W(1.60) multiple sequence alignment

Humlbpa         M---MGALARALPS-ILLALLLTSTPEALGA-NPGLVARITDKGLQYAAQEGLLALQSEL
Rablpb          M---MGTWARALLGSTLLSLLLAAAPGALGT-NPGLITRITDKGLEYAAREGLLALQRKL
Ratlbp          M---MKSATGPLLP-TLLGLLLLSIPRTQGV-NPAMVVRITDKGLEYAAKEGLLSLQREL
Humcetp         M---MLAATVLT---LALLGNAHACSKGTSH-EAGIVCRITKPALLVLNHETAKVIQTAF
Maccetp         M---MLAATVLT---LALLGNVHACSKGTSH-KAGIVCRITKPALLVLNQETAKVIQSAF
Rabcetp         -----------------------ACPKGASY-EAGIVCRITKPALLVLNQETAKVVQTAF
Humbpi          MRENMARGPCNAPRWVSLMVLVAIGTAVTAAVNPGVVVRISQKGLDYASQQGTAALQKEL
Bovbpi          M---MARGPDTARRWATLVVLAALGTAVTTT-NPGIVARITQKGLDYACQQGVLTLQKEL

Humlbpa         LRITLPDFTGDLRIPHVGRGRYEFHSLNIHSCELL
Rablpb          LEVTLPDSDGDFRIKHFGRAQYKFYSLKIPRFELL
Ratlbp          YKITLPDFSGDFKIKAVGRGQYEFHSLEIQSCQLR
Humcetp         QRASYPDITGEKAMMLLGQVKYGLHNIQISHLSIA
Maccetp         QRANYPNITGEKAMMLLGQVKYGLHNIQISHLSIA
Rabcetp         QRAGYPDVSGERAVMLLGRVKYGLHNLQISHLSIA
Humbpi          KRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLP
Bovbpi          EKITIPNFSGNFKIKYLGKGQYSFFSMVIQGFNLP

Programs accepting clustal format input may or may not allow/enforce the following:

Header line may not be required, or just a blank line may be required. Usually the CLUSTAL keyword is required, and sometimes a specfic version number as above may be required.
Number of blank lines between blocks usually does not matter.
Many programs tolerate(and discard) number lines or other kinds of annotation between the blocks starting with blanks in the label field.
Most display programs accept characters other than - within the alignment. Other programs may be more fussy.
Invariably must be the same number of characters per sequence within a particular block. Programs may allow variable white space such that first characters for each sequence in block do not need to be vertically aligned.
Number of characters per block generally flexible (from one block to the next).
All labels must appear in all blocks in same order.
No spaces allowed in labels.
Labels traditionally limited to 10 characters. Other programs on input of aln files may cut longer labels to 10 characters.
Many programs will error-check for redundant labels. This may include after truncation to 10 characters.

Some versions of clustalw allow some options in the output.

May allow longer labels.
Put a line under bottom of block indicating conserved positions.
Put a coordinate after the end of each line.

Last updated 4/4/2008 - Steve Hardies