Clustal W/X
Clustal W (Thompson et al. 1994) is a program for global multiple sequence alignment. It uses a progressive alignment algorithm with affine gap penalties and a guide tree based on sequence similarity to align DNA or amino acid sequences. The affine gap cost model penalizes insertions and deletions using a linear function in which one term is length independent, and the other is length dependent. Gap penalty = Gapopen + Len * Gapextend. There are several recent reviews comparing multiple alignment algorithms (e.g., Hickson et al. 2000, Thompson et al. 1999, and McClure et al. 1994). Morrison and Ellis (1997) discuss the effects of nucleotide sequence alignment on the estimation of phylogenetic hypotheses. The current version is Clustal W2 (Larkin et al. 2007). The program is also available with a graphical user interface, Clustal X.
The method Clustal uses to construct the alignment is called pairwise progressive sequence alignment. This heuristic method first does a pairwise sequence 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 2.0.11
Input data file formats
CLUSTAL, FASTA
Instructions
To run Clustal W2 in the terminal, type:
Clustal W2 is available for several computing platforms.
To run Clustal W2 on your own machine:
Mac OS X: Download Clustal W2 (clustalw-mac-universal-2.0.tgz) and follow the "Install on Mac OS X" instructions in the file:
Windows: Download Clustal W2 (clustalw-windows-xp-2.0.zip) and open:
Online help is available. Within the program there is extensive, context sensitive help.
Online help for command line parameters is also available.
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 2.0.11
Input data file formats
CLUSTAL, FASTA
Instructions
To run Clustal X2 in the terminal, type:
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:
Windows: Download Clustal X2 (clustalx-windows-xp-2.0.zip) and open:
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.
