ClustalW - Revision history

Christoph at 20:40, 6 November 2008

2008-11-06T20:40:25Z

Christoph: /* References */

2008-09-22T03:35:54Z

‎References

Christoph at 03:29, 22 September 2008

2008-09-22T03:29:43Z

Christoph: /* Examples */

2008-05-08T00:18:43Z

‎Examples

Christoph at 21:31, 29 February 2008

2008-02-29T21:31:16Z

Christoph at 07:14, 30 July 2007

2007-07-30T07:14:26Z

Christoph at 21:48, 24 May 2007

2007-05-24T21:48:09Z

Show changes

Christoph at 08:42, 29 December 2006

2006-12-29T08:42:57Z

Christoph: /* References */

2006-12-22T01:12:06Z

‎References

Christoph: /* Usage */ "Bash"

2005-12-30T02:28:11Z

‎Usage: "Bash"

@@ Line 5: / Line 5: @@
 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.<ref name=Thompson1994>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(22):4673-80''. pmid:7984417.</ref>
-<blockquote>'''Note''': The latest version is '''[http://www.clustal.org/download/current/ 2.0.9]''' (2008-06-23)</blockquote>
+<blockquote>'''Note''': The latest version is '''[http://www.clustal.org/download/current/ 2.0.10]''' (2008-10-14)</blockquote>
 == Usage ==

@@ Line 249: / Line 249: @@
 <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.
+* 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.
-* 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.
+* 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.
-* Higgins DG, Sharp PM (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. ''Gene, 73(1):237-44''. pmid:3243435.
+* 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.
 ==External links==

@@ Line 4: / Line 4: @@
 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.<ref name=Thompson1994>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(22):4673-80''. pmid:7984417.</ref>
 == Usage ==
@@ Line 10: / Line 12: @@
 * 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),
-<pre>
+ mkdir Clustal
-mkdir Clustal
+ cd Clustal
-cd Clustal
+ mkdir ClustalW
 mkdir ClustalW
-</pre>
 * Compile source files
-<pre>make</pre>
+ make
 * Add binary path to environment. For example, in a [[Bash|bash]] console, edit the <tt>.bashrc</tt> file and add the following:
-<pre>export PATH=/path/to/clustalw/binary:$PATH</pre>
+ export PATH=/path/to/clustalw/binary:$PATH
 Installation complete!

← Older revision		Revision as of 00:18, 8 May 2008
Line 198:		Line 198:

	==Examples==		==Examples==
		+	*Generate a DNA alignment file
		+	$ clustalw -align -type=dna -infile=foo.fasta > /dev/null
		+	$ cat foo.aln
		+	CLUSTAL W (1.8) multiple sequence alignment
		+
		+	foobar1 AGGTTGTATACTATC
		+	foobar3 AGGTTGT--ACTATC
		+	foobar2 AGGTTGTTTACTATC
		+	foobar4 CGGTTGT--ACTATC
		+	**** ****
		+	*Generate a [[Newick phylogenetic tree format\|Newick tree]] file
		+	$ clustalw -tree -infile=foo.aln > /dev/null
		+	$ cat foo.ph
		+	(
		+	(
		+	foobar1:0.01667,
		+	foobar3:-0.01667)
		+	:0.01667,
		+	foobar2:0.01667,
		+	foobar4:0.06026);
		+
		+	===ClustalV===
	''Note: These examples use the VAX/VMS $ prompt; otherwise, command-line usage is the same on all machines except the Macintosh.''		''Note: These examples use the VAX/VMS $ prompt; otherwise, command-line usage is the same on all machines except the Macintosh.''

@@ Line 230: / Line 230: @@
 * 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.
 [[Category:Bioinformatics]]

@@ Line 198: / Line 198: @@
 ==Examples==
-<pre>
+''Note: These examples use the VAX/VMS $ prompt; otherwise, command-line usage is the same on all machines except the Macintosh.''
 These examples use the VAX/VMS $ prompt; otherwise, command-line
 usage is the same on all machines except the Macintosh.
+*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      OR     $ clustalv /infile=proteins.seq
+ $ clustalv proteins.seq
-Read whatever sequences are in the file "proteins.seq" and do a full
+*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"):
-multiple alignment; output will go to the files: "proteins.dnd"
+ $ clustalv proteins.seq/ktup=2/matrix=pam100/output=pir
-(dendrogram) and "proteins.aln" (alignment).
-$ clustalv proteins.seq/ktup=2/matrix=pam100/output=pir
+*Take the sequences in proteins.pir (they MUST BE ALIGNED ALREADY) and calculate a phylogenetic tree using Kimura's correction for distances:
-Same as last example but use K-Tuple size of 2; use a PAM 100
+*Same as the previous example, EXCEPT THAT AN ALIGNMENT IS DONE FIRST:
-protein weight matrix; write the alignment out in NBRF/PIR format
+ $ clustalv proteins.pir/align/tree/kimura
-(goes to a file called "proteins.pir").
-$ clustalv /profile1=proteins.seq/profile2=more.seq/type=p/fixed=11
+==See also==
-Take the alignment in "proteins.seq" and align it with "more.seq"
+==References==
-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.
-</pre>
-−
 == References ==
 <references/>
 '''Further reading'''

@@ Line 1: / Line 1: @@
-'''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.
+'''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.<ref name=Higgins1992>Higgins DG, Bleasby AJ, Fuchs R (1992). CLUSTAL V: improved software for multiple sequence alignment. ''Comput Appl Biosci, 8(2):189-91''. pmid:1591615.</ref>
-The main new features are a greatly improved (more sensitive) multiple alignment procedure for proteins and improved support
+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.<ref name=Thompson1994>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(22):4673-80''. pmid:7984417.</ref>
 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.
+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.<ref name=Thompson1994>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(22):4673-80''. pmid:7984417.</ref>
 == Usage ==
@@ Line 86: / Line 85: @@
 === 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
+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.
 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
+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.
 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) ===
@@ Line 97: / Line 94: @@
 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: <tt>interactive</tt>. For an example:
-<pre>clustalw -quicktree -interactive</pre>
+ 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:
-<pre>clustalw -options</pre>
+ clustalw -options
 This will return a list with no explanation.
@@ Line 109: / Line 106: @@
 === Command Line Interface ===
-'''Note: The following is taken directly from the "clustalv.doc" file. It will be edited later.'''
+'''Note: The following is taken directly from the "<code>clustalv.doc</code>" file. It will be edited later.'''
 <pre>
@@ Line 287: / Line 284: @@
 == References ==
 * 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.
-[[Category:Academic Research]]
+[[Category:Bioinformatics]]