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ClustalW is a widely used multiple sequence alignment computer program. This program is available from the Clustal Homepage or European Bioinformatics Institute ftp server.

This program accepts a wide range on input format. Included NBRF/PIR, FASTA, EMBL/Swissprot, Clustal, GCC/MSF, GCG9 RSF, and GDE.

There are three main steps:

  1. Do a pairwise alignment
  2. Create a phylogenetic tree (or use a user-defined tree)
  3. Use the phylogenetic tree to carry out a multiple alignment

Users can align the sequences using the default setting, but occasionally it may be useful to customize one's own parameters.

The main parameters are the gap opening penalty, and the gap extension penalty.

The following figure shows the first 90 positions of a protein multiple sequence alignment of instances of the acidic ribosomal protein P0 (L10E) from several organisms.