ClustalX

   
    It is an X windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analyzing the results. The sequence alignment is displayed in a window on the screen. It also provides a versatile coloring scheme which has been incorporated to allow one to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment.

Here is the link to read more about ClustalX:

 http://bips.u-strasbg.fr/fr/Documentation/ClustalX/

    The CLUSTAL programs perform multiple sequence alignments using hierarchical clustering. ClustalW is the direct successor of ClustalV. These programs perform multiple DNA or protein alignments by first doing all possible pairwise alignments, constructing a distance tree, and then aligning sequences based on their order in the tree. ClustalW can be run from the  command line by typing 'clustalw'.  ClustalX is a graphic interface to clustalw. It can be launched from GDE, or from the workspace menu, (Alignment --> ClustalX'), or from the command line ('clustalx')

Here is a technical paper on The Clustal_X windows interface

Thompson, Julie D., Gibson, Toby J., Plewniak Frederick., Jeanmougin, Francois., Higgins, Desmond G.  Department of Biochemistry, University College, Cork, Ireland. Revised and accepted October 28, 1997

    ClustalX: Alignment by Hierarchial clustering:-

The same sequences can be aligned using CLUSTALX by selecting the unaligned proteins, and choosing 'Alignment --> clustalx'. Clicking OK will bring up the unaligned sequences in CLUSTALX:

    The first step in a multiple alignment using CLUSTALX is to perform all pairwise alignments between sequences. Choose 'Alignment --> Alignment Parameters --> Pairwise Alignment Parameters'. This menu lets you choose gap penalties and scoring matrices.

    Next, 'Alignment --> Alignment Parameters --> Multiple Alignment Parameters' allows the choice of similar parameters for building the multiple alignment from the pairwise alignments. Although the default parameters are the same, it is possible that parameters might be adjusted at this stage for more closely-related sequences, since adjacent sequences in an alignment are more likely to be closely-related to each other.

    Finally, for amino acid sequences, 'Alignment --> Alignment Parameters --> Protein Gap Parameters' allows the setting of gap penalties dependent on structural or chemical criteria.

To begin the alignment, choose 'Alignment --> Do Complete Alignment'.

Additional documents

Here is a link for the Clustal-X windows interface file

http://cbif.nmsu.edu/documents-and-files/software-resources/molecular-sequence-analysis-2/thompson-1997a.pdf