Multiple Sequence Alignment and Analysis with Jalview

Navigating the Jalview desktop

Loading protein sequences and alignments into Jalview

Editing gaps in an alignments using Jalview

Colouring protein residues in an alignment using Jalview

Selecting residues, sequences and columns in Jalview

Selecting and exporting groups of residues in sequence alignments using Jalview

Reordering and hiding sequences in an alignments using Jalview

Calculating and Displaying Trees in Jalview

PyMol, ChimeraX and more 3D viewers in Jalview

What is Jalview?

Principal components analysis of protein and nucleotide alignments in Jalview

Customising the appearance of the Jalview alignment window for figure generation

Secondary structure in Jalview using AlphaFold and JPred

3D Molecular Structure Jmol and UCSF Chimera viewers in Jalview

Jalview’s context menus

🎄Fast sequence scanning with Jalview