iiinova — where your digital self keeps evolving

Jalview @jalview.bsky.social · 25/09/2026

This week, we trained new University of Dundee research students exploring areas in 🧫 biology, 🪴plant sciences, 🧬bioinformatics, 🦷 dentistry & 🤰reproductive medicine. From sequence alignment & analysis to 3D structure discovery, we explored how Jalview can support their research. Happy Jalviewing!

Three female students using Jalview, with the PC of the nearest student showing the Jalview desktop with a multiple sequence alignment shaded using the turn propensity colour scheme developed using mathematical values computed by Peter Y. Chou and Gerald D. Fasman in the 1970s.

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Jalview @jalview.bsky.social · 18/09/2026

📂 Who says iPhones have all the folding fun? If your alignment is wider than your screen, try Jalview’s ‘Wrap’ feature! Fold long alignments neatly into your window — then add scales on the left, right or top to create polished figures for papers, seminars & tutorials. ⬇️ www.jalview.org/download/

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Jalview @jalview.bsky.social · 15/09/2026

👓 Visualising sequence alignments in 3D? Jalview enables multiple structures to be visualised with Chimera, ChimeraX, PyMOL and Jmol — helping scientists and educators bring biology to life. 📺 Explore the editor's functionality: www.youtube.com/watch?v=pbms... www.youtube.com/watch?v=yRBL...

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Jalview @jalview.bsky.social · 11/09/2026

📝 Quick tip: You can find the number and length of sequences in your Jalview alignment from the 'View' menu! Select 'Alignment properties' and discover a wealth of information, including: 🧮 Total number of sequences 🧮 Minimum sequence length 🧮 Maximum sequence length 🧮 Average length

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Jalview @jalview.bsky.social · 07/09/2026

📣 Calling all sequence sleuths! 📣 Our latest training video investigates how colouring by conservation in Jalview can be used to deduce the locations of intermolecular interactions like salt bridges in a protein family. 📺: www.youtube.com/watch?v=1O34...

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Jalview @jalview.bsky.social · 20/08/2026

✂️ Editing sequence alignments in Jalview is flexible and reversible. Move sequences ↕️, create groups 👥, insert gaps ➖, using both mouse or keyboard. Edits can also be undone! 🎥 Learn how: www.youtube.com/watch?v=FXGI...

Keyboard with finger hovering over the section containing the up, down and left and right keys.

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Jalview @jalview.bsky.social · 05/08/2026

Batches of protein sequences can be submitted to the JPred server for protein secondary structure prediction, with the option to receive a copy of the results via email. 🔗 www.youtube.com/watch?v=yLga... 🔗 www.compbio.dundee.ac.uk/jpred/help.s... 📜 academic.oup.com/nar/article/...

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Jalview @jalview.bsky.social · 31/07/2026

🎩 Sequences can be hidden in Jalview, allowing specific subsets within the alignment to be focused on and analysed. Hiding sequences improves the readability of large MSAs and the presentation of results for publication. 🔗 www.youtube.com/watch?v=9s7W... 🔗 www.jalview.org/tutorial/exe...

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Jalview @jalview.bsky.social · 24/07/2026

📺 Powering off your tech devices for the summer? Learning never stops! You can watch key bioinformatics lectures by Prof. Geoff Barton on the fundamentals of MSA analysis on your TV instead. Plus, a free 1 hour Jalview masterclass by Jalview Co-ordinator, Dr. Jim Procter. 🔗 Links in comments.

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Jalview @jalview.bsky.social · 23/07/2026

📬 Protein and nucleotide structures can be imported into Jalview, mapped on to MSA sequences and visualised in 3D. Our latest training video summarises some of the structure import options available to users. ▶️ Watch it here: www.youtube.com/watch?v=xFUu...

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Jalview @jalview.bsky.social · 16/07/2026

✂️ Sequence redundancy can create bias and slow down the analysis of alignments. With Jalview, you can quickly reduce redundancy by filtering sequences based on percentage identity. Just adjust the threshold slider to your chosen cutoff! Read more: www.jalview.org/tutorial/exe...

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Jalview @jalview.bsky.social · 10/07/2026

💾 Taking a break? Save your work in Jalview! Alignments, annotations, trees, structures, colours, views and more can be preserved in Jalview, enabling you to begin where you left off. ⬇️ Find out more. 🔗 www.youtube.com/watch?v=xT4g...

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Jalview @jalview.bsky.social · 01/07/2026

⚽ As football fever builds, there’s one competition where every nation is poised to win. 📺 Jalview’s YouTube channel has been watched 250,000+ times by scientists, students and bioinformaticians across 150+ countries. 🧬 Why not tune in too? ⬇️ Link below. 🔗 www.youtube.com/@jalviewtrai...

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Jalview @jalview.bsky.social · 23/06/2026

🏊🏼‍♂️ Dive into molecular structures this summer with Jalview’s integrated 3D viewers. Visualize thousands of protein, DNA and RNA structures with PyMOL, Chimera, ChimeraX and Jmol — whether you're an experienced bioinformatician or just getting started! ▶️ Learn more: www.youtube.com/watch?v=pbms...

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Jalview @jalview.bsky.social · 18/06/2026

🗞️ New preprint: Slivka & Slivka-bio — a lightweight framework for turning command-line tools into web services, developed by Jalview, the Dundee Resource and Genentech. 📜 www.biorxiv.org/content/10.6... ⚡Slivka-bio is set to replace JABAWS in a future release.

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Jalview @jalview.bsky.social · 10/06/2026

Explore the adverse effects of genetic mutations in 2D and 3D views by loading the coding DNA of protein sequences. 1️⃣ Jalview's protein-CDS view: www.youtube.com/watch?v=qFMJ... 2️⃣ Feature mapping: www.youtube.com/watch?v=eK6a... 3️⃣ Genomics file imports: www.youtube.com/watch?v=n_lR...

An alignment of ferredoxin proteins in Jalview with associated coding DNA sequences shown above in the split-screen view. Binding sites imported from UniProt are highlighted in pink in all views, including the associated AlphaFold structure displayed on the right in ChimeraX.

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Jalview @jalview.bsky.social · 27/05/2026

⚙️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.

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Jalview @jalview.bsky.social · 21/05/2026

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...

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Jalview @jalview.bsky.social · 13/05/2026

💊 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?...

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Jalview @jalview.bsky.social · 06/05/2026

🧮 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.

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Jalview @jalview.bsky.social · 01/05/2026

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...

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Jalview @jalview.bsky.social · 24/04/2026

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...

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Jalview @jalview.bsky.social · 17/04/2026

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...

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Jalview @jalview.bsky.social · 15/04/2026

💡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...

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Jalview @jalview.bsky.social · 09/04/2026

🔎 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.

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Jalview @jalview.bsky.social · 01/04/2026

📝 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!

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Jalview @jalview.bsky.social · 20/02/2026

🖥️ 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.

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Jalview @jalview.bsky.social · 13/02/2026

📈 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.

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Jalview @jalview.bsky.social · 05/02/2026

🌍 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 ❤️

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Jalview @jalview.bsky.social · 17/12/2025

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

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Jalview @jalview.bsky.social · 11/12/2025

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/

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Jalview @jalview.bsky.social · 05/12/2025

🔍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...

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Jalview @jalview.bsky.social · 04/12/2025

💡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...

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Jalview @jalview.bsky.social · 04/12/2025

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...

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Jalview @jalview.bsky.social · 26/09/2025

🌍 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! ✨

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Jalview @jalview.bsky.social · 18/09/2025

🕵️‍♂️ 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...

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Jalview @jalview.bsky.social · 11/09/2025

🗣️ 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...

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Jalview @jalview.bsky.social · 05/09/2025

🚀 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.

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.

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Jalview @jalview.bsky.social · 07/08/2025

✅ 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...

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.

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Jalview @jalview.bsky.social · 01/08/2025

🚀 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...

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Jalview @jalview.bsky.social · 17/07/2025

📣 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...

A protein sequence alignment in Jalview with reference annotation tracks consisting of the pLDDT score, secondary structure and PAE dowloaded for each sequence where data is available from AlphaFoldDB.

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Jalview @jalview.bsky.social · 02/07/2025

🖼️ 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...

Multiple sequence alignment in Jalview synced with outputs featured in tree, PCA and 3D molecular graphics viewers.

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Jalview @jalview.bsky.social · 03/06/2025

🌼 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!

Jalview, Daffodil DNA and James Hutton Institute exhibition booths at the ASE 2025 Conference in Cupar, Scotland.

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Jalview @jalview.bsky.social · 03/06/2025

💡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...

Alignment algorithms available from within Jalview.

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Jalview @jalview.bsky.social · 15/05/2025

🚀 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...

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Using 3D Beacons to access AlphaFoldDB, PDB and more in Jalview

YouTube video by Jalview & Dundee Resource Online Training

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Jalview @jalview.bsky.social · 07/05/2025

👀 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...

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Jalview @jalview.bsky.social · 23/04/2025

💡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...

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Jalview @jalview.bsky.social · 17/04/2025

💡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!

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Jalview @jalview.bsky.social · 04/04/2025

💡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.

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Jalview @jalview.bsky.social · 11/03/2025

👩‍🎓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

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