Clustal is a widely used multiple sequence alignment computer program. The latest version is 1.83. There are two main variations: In software engineering, software maintenance is the process of enhancing and optimizing deployed software (software release), as well as remedying defects. ... The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 17 European countries. ... The Centre National de la Recherche Scientifique (CNRS) is one of the most prominent scientific research institutions in France. ... University College Dublin - National University of Ireland, Dublin - more commonly University College Dublin (UCD) - is Irelands largest university, with over 20,000 students. ... A software release refers to the creation and availability of a new version of a computer software product. ... To meet Wikipedias quality standards, this article or section may require cleanup. ... Unix or UNIX is a computer operating system originally developed in the 1960s and 1970s by a group of AT&T Bell Labs employees including Ken Thompson, Dennis Ritchie, and Douglas McIlroy. ... Linux (also known as GNU/Linux) is a Unix-like computer operating system. ... The first Macintosh computer, introduced in 1984, upgraded to a 512K Fat Mac. The Macintosh or Mac, is a line of personal computers designed, developed, manufactured, and marketed by Apple Computer. ... Microsoft Windows is a range of commercial operating environments for personal computers. ... A software license is a legal agreement which may take the form of a proprietary or gratuitous license as well as a memorandum of contract between a producer and a user of computer software. ... Website - Wikipedia, the free encyclopedia /**/ @import /skins-1. ... First 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms. ... The terms computer program, software program, applications program, system software, or just program are used to refer to either an executable program by both lay people and computer programmers or the collection of source code from which an executable program is created (eg, compiled). ...

• ClustalW: command line interface
• ClustalX: This version has a graphical user interface. It is availabe for Windows, Mac OS and Unix/Linux.

This program is available from European Bioinformatics Institute ftp server. Choose unix for Unix/Linux, mac for Mac OS, or dos for Windows.

Input/Output

This program accepts a wide range on input format. Included NBRF/PIR, Fasta, EMBL/Swissprot, Clustal, GCC/MSF, GCG9 RSF and GDE. In bioinformatics, FASTA format is a file format used to exchange information between genetic sequence databases. ...

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:

1. Do a pairwise alignment
2. Create phylogenetic tree (or use user define tree)
3. 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 guide tree only". It has been suggested that Evolutionary tree be merged into this article or section. ... It has been suggested that Evolutionary tree be merged into this article or section. ...

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.

Setting

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

Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and Higgins,D.G. (1997) The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25:4876-4882.
Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G. and Thompson, J.D. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500.

External links

• Strasbourg Bioinformatics Platform - France
• Des Higgins Home Page, UCD, Dublin, Ireland