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Nucleic Acids Res. 1997 December 15; 25(24): 4876–4882.
PMCID: PMC147148

The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools.


CLUSTAL X is a new windows interface for the widely-used progressive multiple sequence alignment program CLUSTAL W. The new system is easy to use, providing an integrated system for performing multiple sequence and profile alignments and analysing the results. CLUSTAL X displays the sequence alignment in a window on the screen. A versatile sequence colouring scheme allows the user to highlight conserved features in the alignment. Pull-down menus provide all the options required for traditional multiple sequence and profile alignment. New features include: the ability to cut-and-paste sequences to change the order of the alignment, selection of a subset of the sequences to be realigned, and selection of a sub-range of the alignment to be realigned and inserted back into the original alignment. Alignment quality analysis can be performed and low-scoring segments or exceptional residues can be highlighted. Quality analysis and realignment of selected residue ranges provide the user with a powerful tool to improve and refine difficult alignments and to trap errors in input sequences. CLUSTAL X has been compiled on SUN Solaris, IRIX5.3 on Silicon Graphics, Digital UNIX on DECstations, Microsoft Windows (32 bit) for PCs, Linux ELF for x86 PCs, and Macintosh PowerMac.

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Selected References

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  • Feng DF, Doolittle RF. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol. 1987;25(4):351–360. [PubMed]
  • Taylor WR. A flexible method to align large numbers of biological sequences. J Mol Evol. 1988 Dec;28(1-2):161–169. [PubMed]
  • Stockwell PA, Petersen GB. HOMED: a homologous sequence editor. Comput Appl Biosci. 1987 Mar;3(1):37–43. [PubMed]
  • Thirup S, Larsen NE. ALMA, an editor for large sequence alignments. Proteins. 1990;7(3):291–295. [PubMed]
  • Clark SP. MALIGNED: a multiple sequence alignment editor. Comput Appl Biosci. 1992 Dec;8(6):535–538. [PubMed]
  • De Rijk P, De Wachter R. DCSE, an interactive tool for sequence alignment and secondary structure research. Comput Appl Biosci. 1993 Dec;9(6):735–740. [PubMed]
  • Galtier N, Gouy M, Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci. 1996 Dec;12(6):543–548. [PubMed]
  • Higgins DG, Sharp PM. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene. 1988 Dec 15;73(1):237–244. [PubMed]
  • Higgins DG, Bleasby AJ, Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. Comput Appl Biosci. 1992 Apr;8(2):189–191. [PubMed]
  • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. [PMC free article] [PubMed]
  • Higgins DG, Thompson JD, Gibson TJ. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 1996;266:383–402. [PubMed]
  • Vingron M, Sibbald PR. Weighting in sequence space: a comparison of methods in terms of generalized sequences. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8777–8781. [PubMed]
  • Henikoff S, Henikoff JG. Position-based sequence weights. J Mol Biol. 1994 Nov 4;243(4):574–578. [PubMed]
  • Thompson JD, Higgins DG, Gibson TJ. Improved sensitivity of profile searches through the use of sequence weights and gap excision. Comput Appl Biosci. 1994 Feb;10(1):19–29. [PubMed]
  • Benner SA, Cohen MA, Gonnet GH. Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng. 1994 Nov;7(11):1323–1332. [PubMed]
  • Notredame C, Higgins DG. SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res. 1996 Apr 15;24(8):1515–1524. [PMC free article] [PubMed]
  • Gotoh O. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol. 1996 Dec 13;264(4):823–838. [PubMed]
  • Parry-Smith DJ, Attwood TK. SOMAP: a novel interactive approach to multiple protein sequences alignment. Comput Appl Biosci. 1991 Apr;7(2):233–235. [PubMed]
  • Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJ. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J Mol Biol. 1987 Jun 20;195(4):957–961. [PubMed]
  • Smith RF, Smith TF. Automatic generation of primary sequence patterns from sets of related protein sequences. Proc Natl Acad Sci U S A. 1990 Jan;87(1):118–122. [PubMed]
  • Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 1991;9(1):56–68. [PubMed]
  • Brouillet S, Risler JL, Hénaut A, Slonimski PP. Evolutionary divergence plots of homologous proteins. Biochimie. 1992 Jun;74(6):571–580. [PubMed]
  • Birney E, Thompson JD, Gibson TJ. PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames. Nucleic Acids Res. 1996 Jul 15;24(14):2730–2739. [PMC free article] [PubMed]
  • Schuler GD, Altschul SF, Lipman DJ. A workbench for multiple alignment construction and analysis. Proteins. 1991;9(3):180–190. [PubMed]
  • Vingron M, Argos P. Motif recognition and alignment for many sequences by comparison of dot-matrices. J Mol Biol. 1991 Mar 5;218(1):33–43. [PubMed]
  • Friemann A, Schmitz S. A new approach for displaying identities and differences among aligned amino acid sequences. Comput Appl Biosci. 1992 Jun;8(3):261–265. [PubMed]
  • Livingstone CD, Barton GJ. Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci. 1993 Dec;9(6):745–756. [PubMed]

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