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Jalview

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Jalview is a free program for multiple sequence alignment editing, visualization and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principle components analysis (PCA) plots and explore molecular structures and annotation.

  • JalviewLite is the web based version of Jalview, and used on many web sites
  • The Jalview Desktop is for biologists and bioinformaticians who need to create, curate, analyse and publish multiple sequence alignments.

Jalview Schema

Jalview has built in DNA, RNA and protein sequence and structure visualization and analysis capabilities, and uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. The Jalview Desktop can also connect with databases and analysis services, and provides a graphical interface to the alignment and analysis services provided by the JavA Bioinformatics Analysis Web Services framework.