| Clustal X |
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Clustal X (Thompson et al.
1997) is a version of Clustal W with a graphical user interface. The current version is Clustal X2 (Larkin et al. 2007). The program is designed to (1) perform multiple alignments, (2) view the results of the alignment process, and (3) if necessary, improve the alignment. Improving the alignment is facilitated by options that are not available in Clustal W (e.g., selecting a section of the alignment to be realigned with different gap penalties, while keeping the rest of the alignment fixed).
The method Clustal uses to construct the alignment is called pairwise progressive sequence alignment. This heuristic method first does a pairwise sequences alignment for all the sequence pairs that can be constructed from the sequence set. A dendrogram (guide tree) of the sequences is then done according to the pairwise similarity of the sequences. Finally a multiple sequence alignment is constructed by aligning sequences in the order, defined by the guide tree.
Version 2.0.9
Input data file formats
CLUSTAL, EMBL/Swiss Prot, FASTA, GCG-MSF, NBRF/PIR
Instructions
To run Clustal X2 in the terminal, type:
clustalx
Clustal X2 is available for several computing platforms.
To run Clustal X2 on your own machine:
Mac OSX: Download Clustal X2 (clustalx-mac-universal-2.0.dmg) and open the file:
ClustalX2.0
Windows: Download Clustal X2 (clustalx-windows-xp-2.0.zip) and open:
clustalx2.exe
From the Clustal X window you can use the pull-down menus to import sequences, align sequences, save sequences or alignments, and perform other program tasks.
Within the program there is an
extensive, context sensitive help.
Sample files for the demonstration:
cteno_DNA.fasta
cteno2_DNA.fasta
cteno13_DNA.fasta
Additional nucleotide sample files are available for download.
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