Multiple sequence alignment with the Clustal series of programs

Nucleic Acids Res. 2003 Jul 1;31(13):3497-500. doi: 10.1093/nar/gkg500.


The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the robustness, portability and user-friendliness of the programs. New features include NEXUS and FASTA format output, printing range numbers and faster tree calculation. Although, Clustal was originally developed to run on a local computer, numerous Web servers have been set up, notably at the EBI (European Bioinformatics Institute) (

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Internet
  • Nucleic Acids / chemistry
  • Phylogeny
  • Sequence Alignment / methods*
  • Sequence Analysis
  • Sequence Analysis, Protein / methods*
  • Software*


  • Nucleic Acids