The exercises demonstrated in these videos can be found in the Jalview manual.

The manual can be viewed on your browser or downloaded from the documentation page on the website.

The URLs featured in the videos are: https://www.jalview.org/tutorial/alignment.fa

https://www.jalview.org/examples/estrogenReceptorProtein.fa

https://www.jalview.org/examples/estrogenReceptorCdna.fa

https://www.jalview.org/tutorial/unaligned.fa

(A) Getting Started playlist

Video 1: What is Jalview multiple sequence alignment software?

Video 2: Navigating the Jalview interface

Video 3: How to launch Jalview on your computer - currently being updated

The download section includes videos showing how to install Jalview on Windows, Mac, Linux, unix and other platforms.

Video 4: Loading sequences and alignments into Jalview

Video 5: Saving sequence alignments and projects in Jalview

Video 6: Jalview’s context menus

(B) Selecting and Editing Sequences playlist

Video 7: Selecting residues, sequences and columns in Jalview

Video 8: Selecting and exporting groups in sequence alignments using Jalview

Video 9: Reordering and hiding regions in sequence alignment using Jalview

Video 10: Editing gaps in alignments using Jalview

(C) Colour, Appearance and Figure Generation playlist

Video 11: Colouring sequence residues and alignments using Jalview

Video 12: Customising the appearance of the Jalview alignment window for figure generation

Video 13: Exporting data and saving images in Jalview

(D) Analysis and Annotation playlist

Video 14: Multiple sequence alignment and analysis with Jalview

Video 15: Principal components analysis of alignments in Jalview

Video 16: Calculating and displaying trees in Jalview

Video 17: Accessing Jmol and UCSF Chimera 3D molecular structure viewers in Jalview

Video 18: Secondary structure prediction of proteins in Jalview

Video 19: Protein disorder predictors in Jalview

(E) Features and Annotation playlist

Video 20: Displaying sequence features in Jalview

Video 21: Annotation rows in Jalview

(F) Genome to Function playlist

Genome to Function Video 1 - View Protein Sequence & its coding DNA

Genome to Function Video 2 - Viewing Ensembl Features on Protein-CDS Alignments

Genome to Function Video 3 - Importing a VCF file & Filtering Variant Features

These videos are hosted on our Jalview Online Training YouTube channel.

(G) AlphaFold and SWISS-MODEL playlist

Viewing AlphaFold models in Jalview

These videos are hosted on our Jalview Online Training YouTube channel.