Jalview

Jalview is a free, open-source, multiple sequence alignment editor, visualizer, and analysis platform written in Java. Primarily used in bioinformatics and computational biology, Jalview allows users to load, edit, analyze, and visualize multiple sequence alignments of DNA, RNA, and protein sequences. Its core functionality includes sequence annotation, phylogenetic tree display and manipulation, principal component analysis (PCA), and integration with remote databases and services. Jalview supports various alignment formats and provides interactive features for sequence manipulation and analysis, facilitating biological research and discovery. It also offers features for calculating conservation scores and highlighting residues based on user-defined criteria. Jalview aims to provide an intuitive interface for both novice and experienced users in the field of sequence analysis.