Christoph at 08:45, 29 December 2006

2006-12-29T08:45:31Z

Christoph: Started article

2005-12-31T01:08:46Z

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'''ClustalX''' is the graphical user interface version of [[Clustal]]. It is availabe for free for Windows, Mac OS and Unix/Linux.

== Using ClustalX to build [[Phylogenetics|Phylogenetic trees]] ==

''Note: This is '''only''' to give the user a very basic introduction to phylogenetic tree building techniques.''

Calculating a phylogenetic tree using ClustalX involves the five steps listed below (all of the necessary commands are located in the 'Trees' menu):

# Remove the regions of the alignment with gaps: select 'delete positions with gaps'.
# If your sequences are less than ~95% identical, you should choose to correct your distance measures for mutiple substitutions: 'correct for multiple substitutions'.
# Make sure you have the correct format for the output:
#* follow the 'output format link';
#* change 'bootstrap label options' from 'branches' to 'nodes'; and
#* close
# Calculate the tree by selecting 'bootstrap NJ tree'.
# View the results in a tree-viewing programme, such as Treeview or [[NJplot]].

== 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.
* 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://bips.u-strasbg.fr/fr/Documentation/ClustalX/ '''ClustalX'''] — from Strasbourg Bioinformatics Platform (France).

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

@@ Line 1: / Line 1: @@
-'''ClustalX''' is the graphical user interface version of [[Clustal]]. It is availabe for free for Windows, Mac OS and Unix/Linux.
+'''ClustalX''' is the graphical user interface version of [[Clustal]]. It is available for free for Windows, Mac OS and Unix/[[Linux]].
 == Using ClustalX to build [[Phylogenetics|Phylogenetic trees]] ==
@@ Line 8: / Line 8: @@
 # Remove the regions of the alignment with gaps: select 'delete positions with gaps'.
-# If your sequences are less than ~95% identical, you should choose to correct your distance measures for mutiple substitutions: 'correct for multiple substitutions'.
+# If your sequences are less than ~95% identical, you should choose to correct your distance measures for multiple substitutions: 'correct for multiple substitutions'.
 # Make sure you have the correct format for the output:
 #* follow the 'output format link';
@@ Line 30: / Line 30: @@
 * [http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ '''ClustalX'''] &mdash; from Strasbourg Bioinformatics Platform (France).
 [[Category:Bioinformatics]]
 [[Category:Phylogenetics]]

ClustalX - Revision history

Christoph at 08:45, 29 December 2006

Christoph: Started article