Jalview

Find out more here: www.jalview.org/download

📈 Jalview is cited ~1,000 times/year—but how is it used? A 2024 survey found 70% of studies used Jalview for multiple sequence alignment (MSA). But, it can also be used for secondary structure and disorder prediction, conservation analyses, sequence feature mapping and 3D structure visualization.

With thanks to @wellcometrust.bsky.social, @gjbarton.bsky.social, @foreveremain.bsky.social, @stuartmac44.bsky.social and @khadijasvoice.bsky.social.

🌍 Twelve months of hard work - endless possibilities for world science. Watch our video tribute to the Jalview community for making 2025 such an incredible year for all of us!
(Sound on 🗣️)

Thank you all ❤️

Thank you for your support, Donald! We love making free, reliable, open software tools for the world 💗

Thank you so much for your support, Christian! ❤️

@wellcometrust.bsky.social @gjbarton.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social @khadijasvoice.bsky.social

Jalview team members Geoff, Jim, Khadija, Renia and Ben posing for a festive photo in the School of Life Sciences, University of Dundee!

❄️Thank you so much to all our users and followers worldwide for making 2025 such a memorable year for us! Seasons greetings to all from the Jalview team all the way from wintry Scotland.❄️

We hope to see you in the new year! ❤️

With thanks to @wellcometrust.bsky.social @gjbarton.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social and @khadijasvoice.bsky.social.

Jalview 2.11.5.1 is here!

New features include:
🎁 Enhanced display of secondary structure consensus annotation tracks
🎁 Improved visualization of phylogenetic trees and PCA plots for secondary structures
🎁 Recognition of .a3m files

Download the new version at: www.jalview.org/download/

🔍Trouble viewing alignments? The Jalview overview window gives you the opportunity to spot patterns in your alignments with a single look.

Read more about it at: www.jalview.org/help/html/fe...

We are infinitely grateful for your support, Bungo. Thank you for cheering us on! 💖💖💖

With thanks to @wellcometrust.bsky.social @pdbeurope.bsky.social @ebi.embl.org @gjbarton.bsky.social @bartongrp.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social

💡Beacon of hope!

Did you know Jalview allows you to access thousands of experimental and predicted protein structures programmatically through the 3D Beacons network?

🔽Find out how on our YouTube channel: www.youtube.com/watch?v=ZBDZ...

Working in Drug Discovery ? 💊

A whole host of clinically relevant features can be visualised on sequences in Jalview — allowing for pharmacologically important regions to be identified.

⬇️ Watch our training video to find out how:
www.youtube.com/watch?v=nLIN...

Thank you so much for your support, Christian! 💗💗💗

🌍 This week, we had the pleasure of providing training to the new cohort of life sciences postgraduate students at the University of Dundee. An array of topics were covered from the basics of multiple sequence alignment to AlphaFold structure quality in Jalview.

All the best for the future! ✨

With thanks to
@wellcometrust.bsky.social, @gjbarton.bsky.social, @foreveremain.bsky.social, @stuartmac44.bsky.social and
@khadijasvoice.bsky.social.

🕵️‍♂️ Attention sequence sleuths! 🕵️‍♀️

🔎 Did you know you can detect similar sequences of protein, DNA and RNA in Jalview using PCA? This makes it easier for conserved regions, including functional subgroups, to be identified.

▶️ Watch our training video to find out how: www.youtube.com/watch?v=KdCx...

More information about the JPred server, including help resources, can be found here: www.compbio.dundee.ac.uk/jpred4/help....

🗣️ Did someone say secondary structure?

In this training video, Suzanne demonstrates how JPred4 can be used to perform secondary structure prediction jobs on single protein sequences.

Watch here: www.youtube.com/watch?v=xwTk...

With thanks to @wellcometrust.bsky.social @gjbarton.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social and @khadijasvoice.bsky.social

📥 Ready to upgrade?
Download Jalview 2.11.5 now: jalview.org/download

📌 Note: This is the last minor release in the 2.11 series.
All future features and fixes are heading into Jalview 2.12 - stay tuned!

The new secondary structure annotation tree showcasing all protein secondary structure providers available for sequences in a sample ferredoxin alignment in Jalview 2.11.5.

🚀 Jalview 2.11.5 is here!

New features include:
✅ Tree visualisation for enhanced protein secondary structure analysis
✅ Consensus colouring for alignments and subgroups
✅ Improved command line options for 3D structure visualisation

Plus, key bug fixes and performance improvements.

@wellcometrust.bsky.social @gjbarton.bsky.social @foreveremain.bsky.social @stuartmac44.bsky.social @khadijasvoice.bsky.social @pdbeurope.bsky.social @ebi.embl.org

Jalview CDS-protein split-screen view showing gene and protein products for homogentisate 1,2 dixoygenase (ENSEMBL ID: ENSG00000113924) in 2D and 3D with VCF variants highlighted in red.

✅ Import genomics VCF files and analyse data like a pro!

Watch Mungo as he outlines how genetic variant data can be imported into and visualised in Jalview using our signature CDS-protein split-screen feature.

Link here: www.youtube.com/watch?v=n_lR...

Thanks, guys! Do follow us here for more updates on new features and releases! ✨

So pleased it worked out for you, Joachim! Follow us here for more updates on new features and releases ✨

With thanks to @wellcometrust.bsky.social @gjbarton.bsky.social @bartongrp.bsky.social
@foreveremain.bsky.social @khadijasvoice.bsky.social
@stuartmac44.bsky.social bsky.social
@javierutges.bsky.social and the wider Barton research group.

🚀 Our latest AlphaFold video is out! Find out how you can discover hidden domains in your AlphaFold models using Jalview's PAE-focused cluster analysis.

▶️ Watch the full video here: www.youtube.com/watch?v=pQC8...