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.

Input Format: 


Instructions for All: 

To run Clustal X2 in the terminal, type:

clustalxClustal X2 is available for several computing platforms.

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.

Instructions for Windows: 

Download Clustal W2 ( and open:

Instructions for OSX: 

Download Clustal W2 (clustalx-mac-universal-2.0.tgz) and follow the “Install on Mac OS X” instructions in the file:

Companion Programs: