⚙️Large alignments can be tackled in Jalview by running alignment services using Slivka in Jalview 2.12 (now available via Jalview Develop). Downloading a local copy of JABAWS is another option. ⬇️ See below for links to both.

Protein secondary structure can be inferred using a number of machine learning methods. In our latest training video, we explore how two such methods — AlphaFold and JPred — can be accessed from Jalview to compare and contrast results. ▶️ Watch it here: www.youtube.com/watch?v=x7SH...

💊 Finding druggable protein domains is hard—but AlphaFold's PAE data can help. Jalview lets you import this into alignments, so it can be clustered to understand protein structure better. ➡️ PAE import: youtu.be/jowUEG47F-Q?... ➡️ Domain detection: youtu.be/pQC8LTDCbug?...

🧮 Are you making the most of Jalview’s annotation rows? These visual layers add context for interpreting biological structure & function: conservation, alignment quality, consensus, secondary structure, AlphaFold's pLDDT & PAE. ➡️ Group/user-specific annotations can also be created.

Boost your workflow with Jalview’s 'Find' function! ✅ Locate motifs sequentially or en masse ✅ Designate hits as new features ✅ Copy to other alignments ✅ Visualize rapidly using the 'Overview Window' ⏰ Save time and see the big picture. 📖 Read more: www.jalview.org/help/html/fe...

JPred predicts protein secondary structure from multiple sequence alignments—and you can access it directly from Jalview. Supported file formats include: ✅ MSF ✅ FASTA ✅ BLC Add your email to get notified when your job finishes 🪄 ▶️ Learn more in our training video: www.youtube.com/watch?v=EW6b...

Did you know Jalview can bring your alignments to life in 3D? Experience the beauty of molecular graphics with PyMol, UCSF Chimera, ChimeraX and JMol in the editor. ▶️ Watch our NEW training video for more insights: www.youtube.com/watch?v=pbms...

💡AlphaFold's pLDDT scores can be visualised in Jalview as annotation tracks at the bottom - useful when comparing regions of high confidence across predicted protein structures in alignments. ▶️ For a guided tour of AlphaFold metrics in Jalview, watch: www.youtube.com/watch?v=WVCM...

🔎 Browse extensive libraries of protein structures in Jalview using the 3D Beacons Network. Once imported, these can be colored, superimposed and viewed in 3D in conjunction with alignments. 👓 Synced views provide precision and clarity, allowing you to hone in on regions of importance.

📝 Alignments are much easier to analyse when you can read the sequences better. Jalview allows you to change alignment font size and type from its 'Format' menu. Choose 'Font' to gain access to more than 100 fonts and make your alignments pop in publications and presentations alike!

🖥️ In the right place with the wrong tech? Worry not - Jalview can be installed on MacOS, Windows and Linux- and Unix-based platforms. It can also be dowloaded via Conda and Homebrew and be run in your favourite web browser, making it an ideal choice for alignment analysis across many devices.

📈 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.

🌍 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 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! ❤️

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...

💡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...

🌍 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! ✨

🕵️‍♂️ 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...

🗣️ 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...

🚀 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.

✅ 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...

🚀 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...

📣 Working with AlphaFold's PAE? The latest instalment in our 'Protein Model Quality' series may be of help! Find out how you can visualise the metric with your alignments and 3D structures in Jalview. ▶️ Watch the new training video here: www.youtube.com/watch?v=jowU...

🖼️ Did you know you can export high-quality images from Jalview? Find out how coloured alignments, phylogenetic trees and PCA plots can be turned into vibrant publication-worthy figures - all with the click of a few buttons. ▶️ Watch our training video on the topic: www.youtube.com/watch?v=wSov...

🌼 Jalview and The Daffodil DNA Project were at the 2025 Conference @associationscied.bsky.social this weekend with colleagues from James Hutton. 🧬Lots of chats with folks about all things bioinformatics, DNA sequencing, multiple sequence alignment and protein structure!

💡Alignment aficionados! Ever wondered how to easily use your favourite alignment methods? ClustalO, TCoffee, MAFFT, MUSCLE and more can be accessed from Jalview to align protein, DNA and RNA sequences. ⏩ Refresh your insights with our instructional video: www.youtube.com/watch?v=Majc...

🚀 Structure alert: Discover protein models in Jalview using the 3D Beacons network. Browse thousands of experimental and predicted structures from Protein Data Bank, AlphaFold, SWISS Model and more with the click of a few buttons! ▶️ Watch our instructional video: www.youtube.com/watch?v=ZBDZ...

👀 Visualise pathogenic variants in Jalview's protein-CDS split screen window as you map these onto your favourite 3D molecular viewer! We have PyMol, ChimeraX, UCSF Chimera and JMol available for your analyses. Watch our 'Genome to Function' video to find out how: www.youtube.com/watch?v=e/6a...

💡Protein lovers - a brand NEW video exploring AlphaFold's pLDDT score in Jalview is out! Find out how you can select, hide and colour your alignments using this 3D structure prediction confidence metric. ▶️ Watch the full video here: www.youtube.com/watch?v=WVCM...

💡Calling all visualisation enthusiasts - did you know Jalview can help you bring your alignments to life in more ways than one? Experience the beauty of molecular graphics with four 3D viewers - PyMol, UCSF Chimera, JMol and ChimeraX - all accessible from Jalview!

💡Curious about intrinsically disordered regions in your proteins? Jalview's got answers - FOUR of them, infact! Many disease-associated proteins, including those involved in neurodegenerative disorders (e.g., Alzheimer's and Parkinson's) and cancer, contain IDRs.

👩‍🎓Last month, 60% of our YouTube audience was women. This International Women's Day, we are celebrating all the trailblazing women who watch our training videos online. 💕 Thank you for supporting our educational content! Watch here: www.youtube.com/@jalviewtrai... #IWD2025 #AccelerateAction

❓Got a burning question you'd like to ask us? Help is a few clicks away! ✏️ Simply sign up to Jalview's Discourse and pop in your inquiries. We'll get right back to you! ⬇️ Link below: ⬇️ discourse.jalview.org

✨Fun fact: Jalview can help you predict the secondary structures of proteins consisting of alpha-helices and beta-strands! 💡In this training video, Suzanne introduces the JPred server and explores various prediction methods for sequences. ⤵️ Watch here: www.youtube.com/watch?v=HW3k...

🏅Our award-winning Jalview Schools Workbook can help you power through A Level or AP Biology as you revise for your exams. 🦣 From the coronavirus to the woolly mammoth, we've got many exciting aspects from the world of genomics covered. ⬇️ Check it out today: www.jalview.org/schools/Scho...

💡Did you know you can use Jalview to view the coding DNA of your protein sequences? This can help you explore the effect of genetic mutations on proteins in 3D. The first video of our 'Genome to Function' mini-series shows you how to do this. Watch here: www.youtube.com/watch?v=qFMJ...

All Jalview services should now be back. If you have any problems please contact us for help.

folks. We have a technical issue currently being looked at by @UoD_DTS that is affecting all @dundeeuni @UoDLifeSciences @gjbarton.bsky.social services. More news as we have it...

2024 was a fun year for us at Jalview! We've been busy, so here's a little 'scrapbook' for you to see all the exciting things we got up to last year: www.youtube.com/watch?v=k6Cf...

Just setting up a Jalview presence here on @bsky.app . For more information about Jalview, see www.jalview.org. Jalview core development is carried out in @gjbarton.bsky.social group at the University of Dundee.