Clustal - Revision history

Christoph at 02:18, 13 July 2012

2012-07-13T02:18:58Z

Christoph: /* See also */

2012-07-13T02:17:16Z

‎See also

Christoph: /* Download */

2012-07-13T02:16:20Z

‎Download

Christoph at 18:00, 18 February 2012

2012-02-18T18:00:17Z

Christoph: /* External links */

2008-02-29T21:29:53Z

‎External links

Christoph: /* Download */

2008-02-23T02:57:43Z

‎Download

Christoph at 02:52, 10 February 2007

2007-02-10T02:52:57Z

Christoph at 08:43, 29 December 2006

2006-12-29T08:43:59Z

Christoph: Started article

2005-12-28T22:03:57Z

Started article

New page

'''Clustal''' is a widely used multiple alignment programme with free packages that can rapidly and simply align hundreds of nucleic acid or amino acid sequences.

There are two main variations (bold) and other "improved" variations:
* '''[[ClustalW]]''': command line interface.
* '''[[ClustalX]]''': This is version has a graphical user interface. It is availabe for Windows, Mac OS and Unix/Linux
* ClustalV
* ClustalG: The package is a rewrite of the well-known Clustal series of alignment packages. The main new feature of ClustalG is the recognition of input word sequences of up to six characters.

== Input/Output ==

This program accept wide range on input format. Included NBRF/PIR, [[FASTA format|Fasta]], EMBL/Swissprot, Clustal, GCC/MSF, GCG9 RSF and GDE

The output format can be one or many of the following: Clustal, NBRF/PIR, GCG/MSF, PHYLIP, GDE, NEXUS.

== Multiple sequence alignment ==
There are 3 main steps:
#Do a pairwise alignment
#Create phylogenetic tree (or use user define tree)
#Use the phylogenetic tree to carry out a multiple alignment

These are done automatically when you select "Do Complete Alignment"
Other options are "Do Alignment from guide tree" and "Produce guild tree only"

== Profile alignments ==

Pairwise alignments are computed for all against all sequences, and similarities are stored in a matrix. This is then converted into a distance matrix, where the distance measures reflect the evolutionary distance between each pair of sequences.

From this distance matrix, a guide tree, or phylogenetic tree, for the order in which pairs of sequences are to be aligned and combined with previous alignments is constructed using a neighbour-joining clustering algorithm. Sequences are progessively aligned at each branch point, starting from the least distant pair of sequences.

== Settings ==
Users can align the sequences using the default setting. But sometimes it's useful to customize your own parameters.

The main parameters are the gap opening penalty, and the gap extension penalty.

== References ==
* Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, and Thompson JD (2003). Multiple sequence alignment with the Clustal series of programs. ''Nucleic Acids Research'' '''31''':3497-3500.
* Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, and Higgins DG (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. ''Nucleic Acids Research'' '''24''':4876-4882.
* Higgins DG, Thompson JD, and Gibson TJ (1996). Using CLUSTAL for multiple sequence alignments. ''Methods Enzymol.'' '''266''':383-402.
* Thompson JD, Higgins DG, and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. ''Nucleic Acids Research'' '''22''':4673-4680.
* Higgins DG, Bleasby AJ, and Fuchs R (1992). CLUSTAL V: improved software for multiple sequence alignment. ''CABIOS'' '''8''':189-191.
* Higgins DG and Sharp PM (1989). Fast and sensitive multiple sequence alignments on a microcomputer. ''CABIOS'' '''5''':151-153.
* Higgins DG and Sharp PM (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. ''Gene'' '''73''':237-244.

== Download ==
* This programme (latest version is 1.83) is available from [ftp://ftp.ebi.ac.uk/pub/software/ European Bioinformatics Institute ftp server]. Choose ''unix'' for Unix/Linux, ''mac'' for Mac OS, or ''dos'' for Windows.

== External links ==
* [http://en.wikipedia.org/wiki/Clustal Wikipedia article on '''Clustal''']
* [http://www.ebi.ac.uk/clustalw/ '''ClustalW'''] — from the EMBL
* [http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ '''ClustalX'''] — from Strasbourg Bioinformatics Platform - France
* [http://www.infobiogen.fr/doc/ClustalW/clustalv.html '''ClustalV'''] — from INFOBIOGEN

[[Category:Academic Research]]
[[Category:Bioinformatics]]

@@ Line 33: / Line 33: @@
 The main parameters are the gap opening penalty, and the gap extension penalty.
 ==Download==
@@ Line 52: / Line 43: @@
 ==See also==
 *[[T-Coffee]]
 ==External links==

@@ Line 52: / Line 52: @@
 ==See also==
 *[[T-Coffee]]
 ==External links==

@@ Line 44: / Line 44: @@
 ==Download==
-* This programme (latest version is 2.0.3) is available from [ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ European Bioinformatics Institute ftp server]. Choose ''unix'' for Unix/Linux, ''mac'' for Mac OS, or ''dos'' for Windows.
+*Latest versions:
 ==See also==

@@ Line 50: / Line 50: @@
 ==External links==
 *[http://www.ebi.ac.uk/clustalw/ '''ClustalW'''] &mdash; from the EMBL
 *[http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ '''ClustalX'''] &mdash; from Strasbourg Bioinformatics Platform - France

@@ Line 43: / Line 43: @@
 ==Download==
-* This programme (latest version is 1.83) is available from [ftp://ftp.ebi.ac.uk/pub/software/ European Bioinformatics Institute ftp server]. Choose ''unix'' for Unix/Linux, ''mac'' for Mac OS, or ''dos'' for Windows.
+* This programme (latest version is 2.0.3) is available from [ftp://ftp.ebi.ac.uk/pub/software/clustalw2/ European Bioinformatics Institute ftp server]. Choose ''unix'' for Unix/Linux, ''mac'' for Mac OS, or ''dos'' for Windows.
 ==See also==

@@ Line 4: / Line 4: @@
 * '''[[ClustalW]]''': command line interface.
 * '''[[ClustalX]]''': This is version has a graphical user interface. It is availabe for Windows, Mac OS and Unix/Linux
 * ClustalV
 * ClustalG: The package is a rewrite of the well-known Clustal series of alignment packages. The main new feature of ClustalG is the recognition of input word sequences of up to six characters.

@@ Line 7: / Line 7: @@
 * ClustalG: The package is a rewrite of the well-known Clustal series of alignment packages. The main new feature of ClustalG is the recognition of input word sequences of up to six characters.
-== Input/Output ==
+==Input/Output==
 This program accept wide range on input format. Included NBRF/PIR, [[FASTA format|Fasta]], EMBL/Swissprot, Clustal, GCC/MSF, GCG9 RSF and GDE
@@ Line 13: / Line 13: @@
 The output format can be one or many of the following: Clustal, NBRF/PIR, GCG/MSF, PHYLIP, GDE, NEXUS.
-== Multiple sequence alignment ==
+==Multiple sequence alignment==
 There are 3 main steps:
 #Do a pairwise alignment
@@ Line 22: / Line 22: @@
 Other options are "Do Alignment from guide tree" and "Produce guild tree only"
-== Profile alignments ==
+==Profile alignments==
 Pairwise alignments are computed for all against all sequences, and similarities are stored in a matrix. This is then converted into a distance matrix, where the distance measures reflect the evolutionary distance between each pair of sequences.
@@ Line 28: / Line 28: @@
 From this distance matrix, a guide tree, or phylogenetic tree, for the order in which pairs of sequences are to be aligned and combined with previous alignments is constructed using a neighbour-joining clustering algorithm. Sequences are progressively aligned at each branch point, starting from the least distant pair of sequences.
-== Settings ==
+==Settings==
 Users can align the sequences using the default setting. But sometimes it's useful to customize your own parameters.
 The main parameters are the gap opening penalty, and the gap extension penalty.
-== References ==
+==References==
-* Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, and Thompson JD (2003). Multiple sequence alignment with the Clustal series of programs. ''Nucleic Acids Research'' '''31''':3497-3500.
+* 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 Research 31:3497-3500''.
-* Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, and Higgins DG (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. ''Nucleic Acids Research'' '''24''':4876-4882.
+* Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997). The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. ''Nucleic Acids Research 24:4876-4882''.
-* Higgins DG, Thompson JD, and Gibson TJ (1996). Using CLUSTAL for multiple sequence alignments. ''Methods Enzymol.'' '''266''':383-402.
+* Higgins DG, Thompson JD, Gibson TJ (1996). Using CLUSTAL for multiple sequence alignments. ''Methods Enzymol 266:383-402''.
-* Thompson JD, Higgins DG, and Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. ''Nucleic Acids Research'' '''22''':4673-4680.
+* Thompson JD, Higgins DG, Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. ''Nucleic Acids Research 22:4673-4680''.
-* Higgins DG, Bleasby AJ, and Fuchs R (1992). CLUSTAL V: improved software for multiple sequence alignment. ''CABIOS'' '''8''':189-191.
+* Higgins DG, Bleasby AJ, Fuchs R (1992). CLUSTAL V: improved software for multiple sequence alignment. ''CABIOS 8:189-191''.
-* Higgins DG and Sharp PM (1989). Fast and sensitive multiple sequence alignments on a microcomputer. ''CABIOS'' '''5''':151-153.
+* Higgins DG, Sharp PM (1989). Fast and sensitive multiple sequence alignments on a microcomputer. ''CABIOS 5:151-153''.
-* Higgins DG and Sharp PM (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. ''Gene'' '''73''':237-244.
+* Higgins DG, Sharp PM (1988). CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. ''Gene 73:237-244''.
-== Download ==
+==Download==
 * This programme (latest version is 1.83) is available from [ftp://ftp.ebi.ac.uk/pub/software/ European Bioinformatics Institute ftp server]. Choose ''unix'' for Unix/Linux, ''mac'' for Mac OS, or ''dos'' for Windows.
-== External links ==
+==See also==
-* [http://en.wikipedia.org/wiki/Clustal Wikipedia article on '''Clustal''']
+*[[T-Coffee]]
-* [http://www.ebi.ac.uk/clustalw/ '''ClustalW'''] &mdash; from the EMBL
+*[http://wikiomics.org/wiki/Bioinfo_tutorial Bioinfo tutorial] &mdash; by Wikiomics.org
 * [http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ '''ClustalX'''] &mdash; from Strasbourg Bioinformatics Platform - France
-* [http://www.infobiogen.fr/doc/ClustalW/clustalv.html '''ClustalV'''] &mdash; from INFOBIOGEN
+==External links==
 [[Category:Bioinformatics]]