Harman Patil (Editor)

Clustal

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Written in
  
C++

Type
  
Bioinformatics tool

Developer(s)
  
Des Higgins Fabian Sievers David Dineen Andreas Wilm (all at the Conway Institute, UCD)

Stable release
  
1.2.2 / 1 July 2016; 7 months ago (2016-07-01)

Operating system
  
UNIX, Linux, Mac, MS-Windows

Licence
  
GNU General Public License, version 2

Clustal is a series of widely used computer programs used in Bioinformatics for multiple sequence alignment.

Contents

History

There have been many incarnations of Clustal that are listed below:

  • Clustal: The original software for progressive alignment based on a phylogenetic tree.
  • ClustalV: A rewrite of the original Clustal package that included phylogenetic tree reconstruction on the final alignment for the first time.
  • ClustalW: command line interface
  • ClustalX: This version has a graphical user interface.
  • ClustalΩ (Omega): The current standard version.

    • The papers describing the clustal software have been very highly cited, with two of them amongst the most cited papers of all time.

    The more recent version of the software available for Windows, Mac OS, and Unix/Linux. It is also commonly used via a web interface at its own home page or hosted by the European Bioinformatics Institute.

    Names

    The guide tree in the initial programs was constructed via a UPGMA cluster analysis of the pairwise alignments, hence the name CLUSTAL.cf. The first four versions in 1988 had Arabic numerals (1 to 4), whereas with the fifth version Des Higgins switched to Roman numeral V in 1992.cf. In 1994 and in 1997, for the next two versions, the letters after the letter V were used and made to correspond to W for Weighted and X for X Window.cf. The name omega was chosen to mark a change from the previous ones.

    Function

    All variants of Clustal align sequences by three main steps:

    1. Do a pairwise alignment
    2. Create a guide tree (or use a user-defined tree)
    3. Use the guide 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 phylogeny" and "Produce guide tree only".

    Input/Output

    This program accepts a wide range of input formats, including NBRF/PIR, FASTA, EMBL/Swiss-Prot, 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, or NEXUS.

    Settings

    Many settings can be modified to adapt the alignment algorithm to different circumstances. The main parameters are the gap opening penalty, and the gap extension penalty.

    References

    Clustal Wikipedia
    (Text) CC BY-SA


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