Hands-on Exercises

These exercises were first developed for our training workshops and were integrated into the Jalview manual. Each hands-on exercise is designed to introduce different aspects of Jalview’s capabilities, such as loading, editing, annotating and saving alignments, performing multiple sequence alignments, viewing 3D structures, creating trees and structure prediction analysis.

# 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
Changing Appearance
8 Colouring Alignment
Beginner
9 Altering Alignment Layout
Beginner
10 Graphical Output
Beginner
Multiple Sequence Alignment
11 Multiple Sequence Alignment
Beginner
PCA and Trees
12 Principal Component Analysis
Beginner
13 Trees
Beginner
Structure
14 Viewing Structures with the integrated Jmol Viewer
Beginner
15 Setting Chimera as the default 3D Structure Viewer
Beginner
Predictions
16 Secondary Structure Prediction
Beginner
17 Protein Disorder Prediction
Beginner
Annotations and Features
18 Annotating Alignments
Beginner
19 Creating Features
Beginner