Difference between revisions of "ClustalX"

From Christoph's Personal Wiki
Jump to: navigation, search
(Started article)
 
 
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]] ==
 
== Using ClustalX to build [[Phylogenetics|Phylogenetic trees]] ==
Line 8: Line 8:
  
 
# Remove the regions of the alignment with gaps: select 'delete positions with gaps'.
 
# 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:
 
# Make sure you have the correct format for the output:
 
#* follow the 'output format link';
 
#* follow the 'output format link';
Line 30: Line 30:
 
* [http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ '''ClustalX'''] — from Strasbourg Bioinformatics Platform (France).
 
* [http://bips.u-strasbg.fr/fr/Documentation/ClustalX/ '''ClustalX'''] — from Strasbourg Bioinformatics Platform (France).
  
[[Category:Academic Research]]
 
 
[[Category:Bioinformatics]]
 
[[Category:Bioinformatics]]
 
[[Category:Phylogenetics]]
 
[[Category:Phylogenetics]]

Latest revision as of 08:45, 29 December 2006

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 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):

  1. Remove the regions of the alignment with gaps: select 'delete positions with gaps'.
  2. If your sequences are less than ~95% identical, you should choose to correct your distance measures for multiple substitutions: 'correct for multiple substitutions'.
  3. 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
  4. Calculate the tree by selecting 'bootstrap NJ tree'.
  5. 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

External links