Jalview is a free cross-platform program for multiple sequence alignment editing, visualisation and analysis. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation.
The Jalview Desktop is an application you can launch from the web or install locally. It is designed for the kind of in-depth sequence analysis necessary when exploring new protein or RNA sequence families to understand how their sequence relates to structure and function.
The Desktop can access sequence, alignment, 3D structure and annotation databases, and web services for multiple alignment, protein disorder and secondary structure prediction and functional analysis.
Jalview is able to link views of 3D structures to multiple sequence alignments. Jmol is integrated with Jalview for this, but you can also configure Jalview to use Chimera, ChimeraX and Pymol for 3D structure visualisation.
Alignments can also be linked to RNA secondary structure visualisations with VARNA, also included in the Jalview Desktop.
All your work in the Jalview Desktop can be saved as a Jalview Project. You can create multiple visualizations of the same alignment, making it easy to create figures describing your findings that can be exported as an image, an HTML document or an encapsulated Postscript file.