Biotech > FAQ > ClustalW FAQ (Frequently Asked Questions)

What is Jalview?

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What is Jalview?

Jalview is a mulitple alignment editor that is written entirely in java. It is provided as an option when you retrieve a multiple alignment from ClustalW. To use it, just click on the Jalview gif. It allows you to do things like:

  • Use many different colour schemes
  • Read and write alignments in a variety of formats
  • Order the alignment according to different criteria
  • Draw UPGMA and NJ trees depending on percent identity criteria
  • Remove gapped columns
  • Perform Smith-Waterman alignment of selected sequences
  • Insert/delete gaps using the mouse
  • Cluster sequences using principle component analysis (PCA)
For more information about Jalview, look at

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