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Journal Articles Trends in Biochemical Sciences Year : 1998

Multiple sequence alignment with Clustal X

F. Jeanmougin
  • Function : Author
J.D. Thompson
  • Function : Author
D.G. Higgins
  • Function : Author
T.J. Gibson
  • Function : Author


The Clustal series of programs are widely used for multiple alignment and for preparing phylogenetic trees. The programs have undergone several incarnations, and 1997 saw the release of the Clustal W 1.7 upgrade and of Clustal X, which has a windows interface. Although we like to think that people use Clustal programs because they produce good alignments, undoubtedly one of the reasons for the programs' wide usage has been their portability to all computers. Portability can have a downside, and for many years the Clustal interface has had to be kept simple. Clustal X (Ref. [ 1 ]) now provides a much nicer, graphical user interface (see Fig. 1) for X-, Mac and PC windows, while maintaining portability. It presents alignments in which residue conservation is shown in colour, and has a very useful new tool for marking poor regions of the alignment. In addition, the user can select such regions for realignment. Thus, Clustal X adds further flexibility to the available strategies for preparing multiple alignments.

Dates and versions

hal-00428491 , version 1 (28-10-2009)



F. Jeanmougin, J.D. Thompson, Manolo Gouy, D.G. Higgins, T.J. Gibson. Multiple sequence alignment with Clustal X. Trends in Biochemical Sciences, 1998, 23 (10), pp.403-405. ⟨10.1016/S0968-0004(98)01285-7⟩. ⟨hal-00428491⟩
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