Version

ClustalW version 2.0.11 is available in hippu.csc.fi
ClustalW version 2.0.9 is available in murska.csc.fi

Description

ClustalW is a multiple sequence alignment program for nucleotide and protein sequences. Clustal uses a method 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 is constructed by aligning sequences in the order, defined by the guide tree.

Usage

At CSC, you can use ClustalW through several interfaces:

• With command EMMA in the Embster graphical sequence analysis platform
  

• EMMA a command line interface for ClustalW in the EMBOSS package.

• Native ClustalW in Murska and in Hippu.

  To run the command line ClustalW in Murska or Hippu, first setup the EMBOSS environment and then type 'clustalw' at command prompt.

module load emboss
clustalw

• If you have an X-term connection to Hippu you can also use the Graphical ClustalX-interface. To start the interface, just type:

clustalx

Help

• ClustalX tutorial

• ClustalW publication/ manuscript

• ClustalW home page
  

Reference

Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22):4673-80.

Distribution

You can install ClustalX to your own coputer. Precompiled executables for Windows. Linux and MacOSX can be downloaded from the ClustalW home page.