Hands-on Exercises

The exercise below are designed to introduce different aspects of Jalview’s capabilities: loading, editing, annotating and saving alignments, performing multiple sequence alignments, viewing 3D structures, creating trees and structure prediction analysis.

Each exercise includes links to videos on Jalview’s YouTube channel that demonstrate the same features, and relevant sections of the Jalview Manual. You can also find more information about these capabilities in Jalview’s built-in help.

# Topic/Title Manual Video Experience Level
Launching Jalview
1 Downloading & Installing Jalview
Beginner
2 Navigation
Beginner
Getting Started
3 Loading Sequences
Beginner
4 Saving Alignments
Beginner
5 Hiding and Revealing Regions
Beginner
6 Reordering the Alignment
Beginner
7 Creating Groups
Beginner
8 Editing Alignments
Beginner
9 Keyboard Edits
Beginner
Changing Appearance
10 Colouring Alignment
Beginner
11 Altering Alignment Layout
Beginner
12 Graphical Output
Beginner
13 User Defined Colour Schemes
Beginner
Multiple Sequence Alignment
14 Multiple Sequence Alignment
Beginner
PCA and Trees
15 Principal Component Analysis
Beginner
16 Trees
Beginner
17 Tree-Based Conservation Analysis
Beginner
18 Remove Redundant Sequences
Intermediate
19 Group Conservation Analysis
Intermediate
Structure
20 Viewing Structures with the integrated Jmol Viewer
Beginner
21 Setting Chimera as the default 3D Structure Viewer
Beginner
22 Aligning Structures using the Ferredoxin Sequence Alignment
Intermediate
23 Colouring a Protein Complex to Explore Domain-Domain Interfaces
Intermediate
Predictions
24 Secondary Structure Prediction
Beginner
25 Protein Disorder Prediction
Beginner
Annotations and Features
26 Annotating Alignments
Beginner
27 Creating Features
Beginner
Genome to Function
28 View Protein Sequence & its Coding DNA
Advanced
29 View Ensembl Features on Protein-CDS Alignments
Advanced
30 Import VCF Files & Filter Variant Features
Advanced