• New Jalview Patch Release: 2.11.1.3

    in development news

    The latest patch release for Jalview 2.11.1 is now available via over the air update and the Jalview download page. This release provides patches for critical bugs affecting the Find function, and also affecting alignment and analysis of linked sets of CDS and Protein sequences. New installers are also provided to address problems when installing Jaliew on Windows to locations containing spaces in the path (only affects new installations). As usual, see Jalview Version 2. Read more →

  • Join the Jalview development team ! Applications close 24th October

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    Just quick post to let you all know that the closing date for the Jalview research software engineer/bioinformatician is October 24th ! If you’d like to join Jalview’s development team and help make Jalview and JalviewJS even better, submit a cover letter explaining why you’d like to work on Jalview and your CV (including your software development experience!) via the University of Dundee Jalview Job Advert

  • New Jalview Patch Release: 2.11.1.1

    in development news

    We are pleased to announce that Jalview 2.11.1.1, the first patch release in the 2.11.1 series, is now available as an over the air update. You can also download standalone jars and the source for the new release via https://www.jalview.org/download This patch release includes fixes for critical bugs, and also brings some new features suggested by the Jalview community. Shift+arrow keys navigate to next gap or residue in cursor mode (enable with F2) Support import of VCF 4. Read more →

  • Jalview 2.11 from bioconda and homebrew

    in development news

    We’re pleased to announce Jalview 2.11.0 is now also available for installation via bioconda. Both the bioconda package and homebrew cask provide a ‘jalview’ command line tool that can be used either to launch the GUI or access Jalview’s command line from your own scripts.

  • Jalview 2.11 - new installer and new capabilities!

    in development news

    We are quite excited about the release of Jalview 2.11.0! This major release introduces support for loading VCF files, and new filters and shading models for sequence features. Under the hood, we’ve addressed many bugs, and also made some important changes in the way the Jalview desktop isinstalled and launched. The Jalview Launcher and Update System. Jalview’s new installation model means you’ll only need to download and install Jalview once. Read more →

  • New minor release: Jalview 2.10.5

    in development news

    Jalview 2.10.5 is a minor release that includes critical patches for users working with Ensembl, RNA secondary structure annotation, and those running Jalview on OSX with Java 10. Jalview’s default memory limit increased to 1G. If you have problems starting Jalview 2.10.5 and you have 1G or less physical memory on your machine, you will need to reduce the memory allocated to Jalview. EPS, PNG and SVG export now includes hidden sequence markers, and representative sequences are marked in bold. Read more →

  • New patch release: Jalview 2.10.4b1

    in development news

    The first patch release for Jalview 2.10.4 is now available. It includes the following minor improvments and critical patches: HGVS nomenclature used for variant annotation retrieved from Uniprot Uniprot import fails for some sequences (Cannot import features with multiple variant elements) Clustal files with sequence positions in right-hand column are now parsed correctly Wrap view - export to SVG - IDs shown but not alignment area in exported graphic F2/Keyboard mode edits work when Overview window has input focus Windows specific fixes: Annotation panel set too high when annotation added to view Updated search paths for Chimera default installation Windows File Shortcuts can be dragged onto the Jalview Desktop Drag URL from Chrome, Firefox, IE to Jalview desktop on Windows doesn’t open file: Read more →

  • New minor release: Jalview 2.10.4

    in development news

    We are very pleased to announce that the final release in Jalview’s 2.10 series is now available. This minor release includes a number of critical patches to Jalview’s web service clients, sequence-to 3D structure mapping code and CDS/Protein cross- referencing system. It also fixes critical GUI and scroll-pad issues for Mac users running the latest versions of Java. Jalview 2.10.4 also features new options in the Structure Chooser dialog, and a more efficient rendering pipeline that makes it easier to work with large alignments involving lots of hidden columns and sequence features. Read more →

  • New patch release: Jalview 2.10.3b1

    in development news

    We are pleased to announce the first Jalview release of 2018! The Jalview 2.10.3b1 bugfix release is distributed under a new Open Source codesigning certificate (“Open Source Developer, JAMES PROCTER”) and includes improvements to the web client for EnsemblGenomes, and fixes the following bugs in the Jalview Desktop: Only one structure is loaded when several sequences and structures are selected for viewing/superposing Alignment doesn’t appear to scroll vertically via trackpad and scrollwheel Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment Helix annotation has ‘notches’ when scrolled into view if columns are hidden Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns User preference for disabling inclusion of sequence limits when exporting as flat file has no effect Jalview can be launched via Java Webstart (for anyone with an up to date java installation), downloaded as a locally installable package, and as a source tarball. Read more →

  • Jalview 2.10.2b1 Released

    in development news

    A bugfix release for 2.10.2 is now available. Version 2.10.2b1 has the following new features: Show gaps in overview window by colouring in grey (sequences used to be coloured grey, and gaps were white) Overview tab in Jalview Desktop Preferences Overview updates immediately on increase in size and progress bar shown as higher resolution overview is recalculated Several minor (and not so minor) bugs are also resolved, including problems with retrieval of Ensembl crossreferences for Uniprot sequences, and PDB sequence/structure associations. Read more →

  • Jalview 2.10.2 - faster PCAs, better overview, and much more

    in development news

    This August 2017 release of Jalview introduces new user interface features, improved and more extensible tree and PCA analysis, more robust 3D structure viewing with UCSF Chimera and an updated service client for JABAWS. The full list of bug fixes and new features can be found in the 2.10.2 Release Notes, but the highlights are below. New dialog and faster and more configurable Tree and PCA calculations Menu entries for calculating PCA and different types of tree have been replaced by a single Calculations dialog box. Read more →

  • Jalview Version 2.10.0 Release

    in development news

    Jalview Version 2.10.0 is released today! Launch from our home page. What’s new in Jalview 2.10? Jalview 2.10 is the next major release in the Jalview 2 series. Full details are in the Jalview 2.10 Release Notes, but the highlights are below. Ensembl sequence fetcher Annotated Genes, transcripts and proteins can be retrieved via Jalview’s new Ensembl REST client. Support for import of Ensembl data allows: Read more →

  • Patch Friday: Second Patch release for 2.9

    in development news

    Jalview 2.9.0b2 fixes a Desktop bug where group associated consensus and conservation annotation rows are duplicated when an alignment is partitioned by clicking on the tree viewer. This version of Jalview is also the first to be provided as ‘timestamped’ signed jars. What this means is that Jalview 2.9.0b2 will always be allowed to run on systems that support Java, even after our Certum code signing certificate is no longer valid. Read more →

  • Patch Friday: 2.9.0b1 patch release

    in development news

    We’ve just uploaded the patch release for version 2.9. This new version addresses a dozen or so minor issues in the desktop and applet, including linked editing of cDNA and Protein alignments and exchange of alignment data embedded in HTML pages. As usual, let us know about any problems through our email list or directly via our bug tracker! For the full details, take a look at version 2.9.0b1’s release notes. Read more →

  • Version 2.8.2 Now available!

    in development news

    We are very pleased to announce that Jalview version 2.8.2 is now available (just in time for our Jalview course in London on 15th December!). This release is special for a number of reasons, the most important being that it is the first one produced by our new core development team members Mungo Carstairs and Tochukwu (Charles) Ofoegbu, and also includes features introduced by our 2012 Jalview summer of code student, Anne Menard. Read more →

  • apologies for Jalview launch problems on 3rd-4th November 2014

    in development news

    Unfortunately, due to a configuration error whilst we updated our drupal servers, the Jalview desktop and applet were unavailable for a short period of time, but are now back. We realise here at www.jalview.org that this outage will have inconvenienced many people, and we’ve already begun to take steps to make sure this doesn’t happen again. Thanks for your patience - and stay tuned for the next Jalview release! Version 2. Read more →

  • Jalview Version 2.8.1 Now Available!

    in development news

    Version 2.8.1 of Jalview is now available for download at www.jalview.org. This is the third release in the 2.8.x series of Jalview, and in addition to a liberal scattering of bug fixes, provides new support for RNA secondary structure prediction, additional score models for tree-building and PCA, and several minor improvements to Jalview’s user interface. We’re also proud to highlight features in this release contributed by the Jalview developer community: Read more →