ClustalW

ClustalW is multiple alignment programme for Unix and Linux (I am ignoring other operating systems in this article/tutorial). ClustalW is a major update and rewrite of the ClustalV program which was described in Higgins et al., 1992.

The main new features are a greatly improved (more sensitive) multiple alignment procedure for proteins and improved support for different file formats. This software was described in Thompson et al., 1994.

The usage of ClustalW is largely the same as for ClustalV. Details of the new alignment algorithms are described in the manuscript by Thompson et al., 1994.

Usage

Installation

• Create a directory where you want to store the ClustalW executables and files. Extract files from archive downloaded into this directory. For an example (under your "home" directory),

mkdir Clustal
cd Clustal
mkdir ClustalW

• Compile source files

make

• Add binary path to environment. For example, in a bash console, edit the .bashrc file and add the following:

export PATH=/path/to/clustalw/binary:$PATH

Installation complete!

File input (sequences to be aligned)

The sequences must all be in one file (or two files for a "profile alignment") in ONE of the following formats:

• FASTA (Pearson)
• NBRF/PIR
• EMBL/Swiss Prot
• GDE
• CLUSTAL
• GCG/MSF
• GCG9/RSF

The program tries to "guess" which format is being used and whether the sequences are nucleic acid (DNA/RNA) or amino acid (proteins). The format is recognised by the first characters in the file. This is kind of stupid/crude but works most of the time and it is difficult to do reliably, any other way.

First characters in a file recognised by ClustalW
Format	First non-blank word or character in the file
FASTA	>
NBRF	>P1; or >D1;
EMBL/SWISS	ID
GDE protein	%
GDE nucleotide	#
CLUSTAL	CLUSTAL (blocked multiple alignments)
GCG/MSF	PILEUP or !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT or MSF on the first line, and '..' at the end of line
GCG9/RSF	!!RICH_SEQUENCE

source: ClustalW documentation by EMBL

DNA vs. Protein: the program will count the number of A, C, G, T, U, and N charcters. If 85% or more of the characters in a sequence are as above, then DNA/RNA is assumed, protein otherwise.

File output

The alignments

The alignment output format can be set to: CLUSTAL (a self explanatory blocked alignment). There are other outputs, however, I am only interested in the "CLUSTAL" output.

Notes on "Bootstrapping"

When you use the BOOTSTRAP in ClustalW to estimate the reliability of parts of a tree, many of the uncorrected distances may randomly exceed the arbitrary cut off of 0.93 (sequences only 7% identical) if the sequences are distantly related. This will happen randomly i.e. even if none of the pairs of sequences are less than 7% identical, the bootstrap samples may contain pairs of sequences that do exceed this cut off. If this happens, you will be warned. In practice, this can happen with many data sets. It is not a serious problem if it happens rarely. If it does happen (you are warned when it happens and told how often the problem occurs), you should consider removing the most distantly related sequences and/or using the PHYLIP package instead.

A further problem arises in almost exactly the opposite situation: when you bootstrap a data set which contains 3 or more sequences that are identical or almost identical. Here, the sets of identical sequences should be shown as a multifurcation (several sequences joing at the same part of the tree). Because the Neighbor-Joining method only gives strictly dichotomous trees (never more than 2 sequences join at one time), this cannot be exactly represented. In practice, this is NOT a problem as there will be some internal branches of zero length seperating the sequences. If you display the tree with all branch lengths, you will still see a multifurcation. However, when you bootstrap the tree, only the branching orders are stored and counted. In the case of multifurcations, the exact branching order is arbitrary but the program will always get the same branching order, depending only on the input order of the sequences. In practice, this is only a problem in situations where you have a set of sequences where all of them are VERY similar. In this case, you can find very high support for some groupings which will disappear if you run the analysis with a different input order. Again, the PHYLIP package deals with this by offering a JUMBLE option to shuffle the input order of your sequences between each bootstrap sample.

Summary of the command line usage (very brief)

ClustalW is designed to be run interactively. However, all parameters can be set and run from the command line by giving options after the clustalw command. Options should be preceded by '-'.

If anything is put on the command line, the program will (attempt to) carry out whatever is requested and will exit. If you wish to use the command line to set some parameters and then go into interactive mode, use the command line switch: interactive. For an example:

clustalw -quicktree -interactive

This will set the default initial alignment mode to fast/approximate and will then go to the main menu.

To see a list of all the command line parameters, type:

clustalw -options

This will return a list with no explanation.

To get (very brief) help on command line usage, use the -help or -check options. Otherwise, the command line usage is self explanatory or is explained in clustalv.doc. The defaults for all parameters are set in the file param.h which can be changed easily (remember to recompile the program afterwards).

Command Line Interface

Note: The following is taken directly from the "clustalw.doc" (v.1.83) file. It will be edited later.

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.

-ALIGN

do full multiple alignment

-TREE

calculate NJ 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

-OUTORDER=

INPUT or ALIGNED

-CASE

LOWER or UPPER (for GDE output only)

-SEQNOS=

OFF or ON (for Clustal output only)

-SEQNO_RANGE=

OFF or ON (NEW: for all output formats)

-RANGE=m,n

sequence range to write starting m to m+n.

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=IUB, CLUSTALW or filename

-PWGAPOPEN=f

gap opening penalty

-PWGAPEXT=f

gap opening 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

-ENDGAPS

no end gap separation pen.

-GAPDIST=n

gap separation pen. range

-NOPGAP

residue-specific gaps off

-NOHGAP

hydrophilic gaps off

-HGAPRESIDUES=

list hydrophilic res.

-MAXDIV=n

% ident. for delay

-TYPE=

PROTEIN or DNA

-TRANSWEIGHT=f

transitions weighting

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 OR branch

position of bootstrap values in tree display

Examples

These examples use the VAX/VMS $ prompt; otherwise, command-line 
usage is the same on all machines except the Macintosh.

 
$ clustalv proteins.seq      OR     $ clustalv /infile=proteins.seq

Read whatever sequences are in the file "proteins.seq" and do a full 
multiple alignment; output will go to the files: "proteins.dnd" 
(dendrogram) and "proteins.aln" (alignment).


$ clustalv proteins.seq/ktup=2/matrix=pam100/output=pir

Same as last example but use K-Tuple size of 2; use a PAM 100 
protein weight matrix; write the alignment out in NBRF/PIR format 
(goes to a file called "proteins.pir").


$ clustalv /profile1=proteins.seq/profile2=more.seq/type=p/fixed=11

Take the alignment in "proteins.seq" and align it with "more.seq" 
using default values for everything except the fixed gap penalty 
which is set to 11.  The sequence type is explicitely set to 
PROTEIN.


$ clustalv proteins.pir/tree/kimura

Take the sequences in proteins.pir (they MUST BE ALIGNED ALREADY) 
and calculate a phylogenetic tree using Kimura's correction for 
distances.  


$ clustalv proteins.pir/align/tree/kimura

Same as the previous example, EXCEPT THAT AN ALIGNMENT IS DONE 
FIRST.


$ clustalv proteins.seq/align/boot=500/seed=99/tossgaps/type=p

Take the sequences in proteins.seq; they are explicitely set to be 
protein; align them; bootstrap a tree using 500 samples and a seed 
number of 99.

References

Further reading

• 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(13):3497-500. pmid:12824352.
• Jeanmougin F, Thompson JD, Gouy M, Higgins DG, Gibson TJ (1998). Multiple sequence alignment with Clustal X. Trends Biochem Sci, 23(10):403-5. pmid:9810230.
• Higgins DG, Sharp PM (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene, 73(1):237-44. pmid:3243435.