Jalview has built in DNA, RNA and protein sequence and structure visualization and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structures. Jalview is a free program for multiple sequence alignment editing, visualization and analysis. Edit sequence alignments, analyze them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.
Jalview is a piece of bioinformatics software that was originally written by Michele Clamp whilst working in Geoff Barton’s group at the University of Oxford and European Bioinformatics Institute (EBI). Jalview 2, a re-engineered version produced by Andrew Waterhouse and Jim Procter whilst working in Geoff Barton’s group at the School of Life Sciences, University of Dundee, was released in 200 and its development is supported by the Biotechnology and Biological Sciences Research Council (BBSRC) and Wellcome Trust.
It is used widely by a variety of web servers (e.g. the EBI ClustalW server and the Pfam protein domain database) but is also available as a general purpose alignment editor.
Jalview has a wide range of functions in addition to multiple sequence alignment generation, viewing and editing, including calculating phylogenetic trees and viewing molecular structures. Recent versions of Jalview include features for the analysis of genetic variation from public databases or local Variant Call Format (VCF) files. Jalview connects to many external web services to import data and perform calculations.
The Jalview Desktop provides access to protein and nucleic acid sequence, alignment and structure databases, and includes the Jmol3 and Chimera viewer for molecular structures, and the VARNA4 program for the visualization of RNA secondary structure. It also provides a graphical user interface for the multiple sequence alignment, conservation analysis and protein disorder prediction methods provided as Java Bioinformatics Analysis Web Services (JABAWS).
Its primary function is the editing and visualization of sequence alignments, and their interactive analysis. Tree building, principal components analysis, physico-chemical property conservation and sequence consensus analyses are built into the program. Web services enable Jalview to access online alignment and secondary structure prediction programs, as well as to retrieve protein and nucleic acid sequences, alignments, protein structures and sequence annotation. Multiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring and layout. Alignment views are dynamically linked with Jmol and UCSF Chimera6 structure displays, a tree viewer and spatial cluster display, facilitating interactive exploration of the alignment’s structure. The application provides its own Jalview project file format in order to store the current state of an alignment and analysis windows. Jalview also provides WYSIWYG 7 style figure generation capabilities for the preparation of alignments for publication.