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    Archived pages: 513 . Archive date: 2013-08.

  • Title: What is Jalview ? | jalview.org
    Descriptive info: .. Skip to main content.. Main menu.. Home.. About.. Documentation.. Publications.. Credits.. Advisory Committee.. Help.. FAQ.. Discussion Mailing List.. Community.. News Mailing List.. Links.. Community News.. Development.. Jalview Bug Tracker.. Development Version.. Jalview Git Web.. Version Archive.. Release History.. Development News.. Training.. Training Courses.. Training News.. Download.. Do you use Jalview? Then please take a few minutes to write a letter to us saying how you use Jalview in your research and/or teaching.. We need your letters to support our application to the UK BBSRC to renew core funding for Jalview development.. Please write ideally as a PDF on headed paper and send to:.. support_jalview@bartongroup.. org.. DO NOT use this email address for questions about Jalview.. Thank you!.. Latest News.. Version 2.. 0.. 1 of JABAWS is now available.. Posted On:.. 02-07-2013.. Desktop.. Jalview talk and users meeting in Berlin at ISMB 2013.. Please help with Jalview funding renewal.. 18-04-2013.. General.. View All News.. View all courses.. Jalview is a free program for multiple sequence alignment editing, visualisation and analysis.. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular  ...   VARNA.. to display RNA secondary structure.. The.. Jalview Desktop.. can also connect with databases and analysis services, and provides a graphical interface to the alignment and analysis services provided by the.. J.. av.. A.. B.. ioinformatics.. nalysis.. W.. eb.. S.. ervices.. framework.. Finding out more.. About section.. provides more information, and the links at the top of the page will let you.. launch the Jalview Desktop.. , try out the.. JalviewLite applet.. demonstration pages.. Download page.. lets you get a Jalview Desktop installer for your system, and links to compiled jars and source code.. Availability.. Jalview is an open source project released under the.. GPL.. Its development is coordinated by.. Jim Procter.. and.. Geoff Barton.. in the.. Computational Biology group.. at the.. University of Dundee.. 's.. College of Life Sciences.. with support from the.. UK's Biotechnology and Biological Science Research Council.. Published under.. CC SA v3.. If you use Jalview in your work, please cite this publication:.. Waterhouse, A.. M.. , Procter, J.. B.. , Martin, D.. A, Clamp, M.. and Barton, G.. (2009).. "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench".. Bioinformatics25 (9) 1189-1191.. doi: 10.. 1093/bioinformatics/btp033..

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  • Title: Jalview - Applets
    Descriptive info: JalviewLite Examples.. Applet Parameters.. Javascript API.. in-page API demo.. Two JalviewLites demo.. Jalview and Jmol demo.. JalviewLite is a web based version of Jalview, which runs as a Java applet in or on a web page.. It's one of the easiest ways of providing an interactive display for precalculated alignments, features and annotations files.. It lacks some functionality available in the Jalview Desktop, however, such as making images, saving files, and running web service jobs.. This is mostly due to security restrictions imposed on applets.. Try out JalviewLite by pressing one of the buttons below.. For more information on how to use the applet in  ...   sequences x 150 residues).. User Defined Colours, loads an associated Newick format tree file which is used to sort the alignment, and group consensus and sequence logos are shown below the alignment.. Displays a features file on the alignment.. Associates PDB file 1GAQ with sequence FER1_MAIZE.. Displays a Multiple Sequence Alignment Based JNet Prediction for a Sequence.. RF00031 RFAM Alignment with per sequence secondary structure.. Displays an RFAM RNA fold family with secondary structure annotation.. CC-SA 3.. If you use Jalview in your work, please cite this publication:.. (2009) "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" Bioinformatics 25 (9) 1189-1191..

    Original link path: /examples/applets.html
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  • Title: About | jalview.org
    Descriptive info: Jalview is a free program developed for the interactive editing, analysis and visualization of multiple sequence alignments.. It can also work with sequence annotation, secondary structure information, phylogenetic trees and 3D molecular structures.. JalviewLite and Jalview Desktop.. JalviewLite.. allows sequence alignments to be visualized in a web page, along with annotation, phylogenetic trees, and associated 3D structures.. It has built in support for a wide range of alignment file formats, GFF files, and Jalview's own sequence and alignment annotation format.. It allows editing, and can also show the consensus sequence, sequence logo and amino acid conservation for your alignment.. analysis, tree and principal component analysis calculations.. The other flavour of Jalview is the.. :.. is an application you can launch  ...   and annotation databases, and web services for multiple alignment, protein disorder and secondary structure prediction and functional analysis.. Some of the most important things about the Jalview desktop are that you can save all your work as a Jalview Project, and create multiple visualizations of the same alignment, making it easy to create figures describing your findings that can be exported as an image, an HTML document or an encapsulated Postscript file.. Jalview is Open Source Bioinformatics Software.. Jalview is developed in Java, and the source has always been freely available.. In 2010, we launched Jalview's own git repository, which lets bioinformatics developers from around the world contribute to Jalview.. To find out more, head on over to.. Jalview Development..

    Original link path: /overview.html
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  • Title: Documentation | jalview.org
    Descriptive info: Jalview Help.. Pressing F1 in the Jalview Desktop will open the built-in help system, which can also be searched.. F1 in JalviewLite will open this page in your browser.. How do I edit sequences in Jalview?.. A quick guide to mouse and keystroke alignment editing in Jalview 2.. The Jalview 2.. 7 Manual.. 5MB for on screen..  ...   by David Martin, Jim Procter, Geoff Barton and Andrew Waterhouse.. Old documentation preserved for posterity.. Jalview Quickstart Guide.. A quick reference for Jalview 2.. 0 that was produced for its first release in 2005.. Jalview 1.. 18 Documentation.. The original help documentation for Jalview version 1 (published in Clamp et.. al 2004).. [ just being fixed ;) ]..

    Original link path: /about/Documentation
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  • Title: Publications | jalview.org
    Descriptive info: Peer reviewed publications.. If you use Jalview 2 in your work, please cite Waterhouse.. et al.. To cite an analysis performed with.. JABAWS.. , please use Troshin.. (2011).. Troshin PV, Procter JB, Barton GJ (2011) Java bioinformatics analysis web services for multiple sequence alignment--JABAWS:MSA.. Bioinformatics 27: 2001-2002.. doi:10.. 1093/bioinformatics/btr304.. Waterhouse AM, Procter JB, Martin DMA, Clamp M, Barton GJ  ...   25: 1189-1191.. Thompson JD, Muller A, Waterhouse A, Procter J, Barton GJ, et al.. (2006) MACSIMS: multiple alignment of complete sequences information management system.. BMC Bioinformatics 7: 318.. 1186/1471-2105-7-318.. Clamp M, Cuff J, Searle SM, Barton GJ (2004) The Jalview Java alignment editor.. Bioinformatics 20: 426-427.. 1093/bioinformatics/btg430.. Take a look at the.. citations for the Jalview 2 paper in PubMedCentral..

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  • Title: Credits | jalview.org
    Descriptive info: People and organisations responsible for.. Jalview 2.. ,.. JalView 1.. , and.. www.. jalview.. org design.. are listed below:.. Jalview Version 2 (Developed from 2004 at University of Dundee with support from the BBSRC).. Andrew Waterhouse.. David Martin.. People who have contributed code, or otherwise collaborated with the core Jalview 2 team, in roughly historical order:.. Paolo di Tomasso (.. Center for Genomic Regulation.. , Spain).. Added support for parsing.. T-COFFEE.. score files and displaying them on the alignment, introduced in version 2.. 8.. Jan Engelhart (.. Stadler Bioinformatics Group, University of Leipzig.. , Germany).. Jan was our second.. Google Summer of Code.. student, in 2011, and implemented the RNA structure consensus logo, and embedded.. in the Jalview v2.. 8 desktop.. Lauren Lui (.. Lowe Lab, University of California at Santa Cruz.. , USA).. Lauren was our first.. student in 2010, and implemented the RNA secondary structure annotation, and RNA helix colour scheme introduced in version 2.. Bernd  ...   version 2.. 1.. Andreas Prlic (originally at.. San Diego Supercomputing Center, USA.. Andreas wrote the first Java DAS client library,.. dasobert.. , used in Jalview 2.. 1 through to version 2.. 7, and made many suggestions on how Jalview could better use DAS.. If we've forgotten you, or you'd like to update your details,.. Contact us!.. Funding from.. The UK's Biotechnology and Biological Sciences Research Council.. 2009-2014.. BB/G022682/1 The Jalview Resource for Sequence Analysis and Annotation - www.. 2004-2007.. BBS/B/16542 Visualisation of Biological Sequences, Alignments and Structures.. (.. VAMSAS.. Jalview Version 1 (Developed from 1996 onwards at Oxford and EMBL-EBI).. Michele Clamp.. James Cuff.. Stephen Searle.. Jalview 2 Logo and Site Design.. The original Jalview 2 logo and site design was created by Andrew Waterhouse in 2005.. The Jalview logotype was created in 2012 by.. Barry Strachan.. Site design and development by Ryan McLaughlan and Andrew Millar in the.. Web Services group at Dundee College of Life Sciences..

    Original link path: /about/credits
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  • Title: Jalview Scientific Advisory Committee | jalview.org
    Descriptive info: Jalview Scientific Advisory Committee.. The Jalview Scientific Advisory Committee.. The committee meets regularly to discuss the current and future directions for Jalview.. Current Members.. Research Computing at the Conte Centre, Harvard University, USA.. Toby Gibson.. European Molecular Biology Laboratory, Heidelberg, Germany.. Daniel Rigden.. School of Biological Sciences, University of Liverpool, UK.. Richard Baldock.. MRC Human Genetics Unit, University of Edinburgh, UK.. Michael Gribskov.. Department of Biological Science, Purdue University, USA..

    Original link path: /about/jalview-scientific-advisory-committee
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  • Title: Help | jalview.org
    Descriptive info: Places to get help when using Jalview !.. The first place to look for help is the.. Jalview Documentation Page.. We also maintain a list of.. Frequently Asked Questions (FAQ).. If you don't find the answer in any of these, then send an email to the.. Jalview Users Discussion list.. Reporting Bugs.. If you think you found a bug, then take a look at the.. FAQ page on Reporting Bugs.. !..

    Original link path: /Help
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  • Title: jalview.org
    Descriptive info: FAQ Menu Block.. How Do I Run Jalview ?.. How do I get the consensus sequence for an alignment?.. F2 key does not toggle Cursor mode on my Mac?.. Is there a quick reference for Jalview?.. Does Jalview work with nucleotide sequences and alignments?.. Why can t I save files or images from the Applet version?.. Can I run Jalview from the command line?.. The old Jalview had font size and page orientation settings for its Postscript output.. Where have they gone?.. How do I increase the memory available to Jalview?.. Something that normally works in Jalview has stopped working! What should I do?.. How do I report a bug in Jalview?.. Can I install Jalview on a server?.. I get Windows Error 3 when installing with InstallAnywhere.. A Jalview file I created in an earlier version of Jalview no longer loads.. InstallAnywhere on Linux fails to find shared libraries.. My application doesn t like the /start-end sequence suffix in files saved by Jalview.. Java Web Start version of Jalview fails with error Unable to Launch - because JAR resources in JNLP are not signed by same cert.. Warning about untrusted or out of date certificate when launching Jalview via Java Webstart.. The Jalview Installer for OSX won t run.. How do I run Jalview?.. You need a computer that can run Java 1.. 6 or later to run the full Jalview application (unfortunately this excludes users with older Macs -.. sorry.. If java is installed, then the 'Launch Jalview Desktop' link at the top should work (if your browser asks you to save the application-x-jnlp file or choose an application to run it with, look for 'Java Web Start', or locate your java installation directory and look for the.. javaws.. binary).. You can also go to the.. Install Anywhere Web Installer download area.. area to get an installer for your platform.. If you don't have Java 1.. 6, but do have Java turned on in your browser, you can try the web based version of Jalview - JalviewLite - right now by going to the.. applets.. page.. The web based version doesn't let you print or access web services, but includes most of Jalview's.. core functionality.. Use the Mouse.. Use the cursor keys.. Edit Selected Region Only.. Press F2 to enter Keyboard Mode.. Right-click on the consensus histogram and select "Copy consensus sequence".. You may be using a keyboard which has visual / audio settings mapped onto the Function keys.. You must press the "Fn" key, together with F2 key to toggle Cursor Mode.. Yes, a quick reference PDF for an early release of Jalview 2 is.. , but we haven't updated it for a while.. Versions of Jalview released before November 2012 did not include any special support for scoring or visualizing nucleotide sequences, although they could read, write and manipulate DNA and RNA sequences, and calculate a consensus.. 8 of Jalview was the first release to include special support for nucleic acid sequences, and included a substitution matrix that copes with both RNA and DNA symbols which can be used to calculate trees and principal component analysis plots from alignments.. Nucleotide base pair patterns provided as WUSS or VIENNA dot-bracket annotation can also be visualised, and used to calculate base-pair consensus score and sequence logos.. 8 of the Jalview Desktop also included.. for interactive exploration of 2D RNA structure.. For the latest information about nucleic acid support, see the.. nucleic acid section of Jalview's help pages.. Because of security restrictions, an applet may not read or write files on the local system.. This is to protect you from a malicious applet storing a virus on your computer or deleting all your files.. Only the Jalview Desktop can create, print or save images, alignment files and Jalview projects on your computer.. You can usually send data you have opened in the JalviewLite applet to the Jalview Desktop using the.. "File - View In Full Application".. menu entry.. This will only work if you can launch the java webstart version of the Jalview Dekstop, and in the current version, will not send any additional edits or other changes to the alignment data that you may have made after opening it in JalviewLite.. Yes.. The Jalview Desktop has a number of command line options, but how you access them depends on the way you want to launch Jalview:.. 1.. If you use Java Web Start to launch Jalview, then on some versions of Java Webstart you can start up Jalview with a specific file by typing:.. javaws.. http://www.. org/webstart/jalview.. jnlp.. -open.. yourFileName.. This is fine for launching the desktop with prepared data, but less useful for batch processing since any console  ...   command line (and if in doubt, also include.. awt.. headless=true.. to tell Java not to attempt to use the graphics environment).. For example:.. jalview.. Jalview -nodisplay -open.. The latest version of Jalview should run fine on a server without a graphics environment, but some operations may fail.. If you encounter problems,.. submit a bug report.. We have tried to ensure that all files created in earlier versions of Jalview can be read in by later versions.. If you have a Jalview format file which no longer loads, please let us know by emailing the file to us.. It is possible other people are having the same problem!.. Some latest versions of Linux fail to install with InstallAnywhere and will generate error messages such as "error while loading shared libraries: libm.. so.. 6: cannot open".. The problem can be fixed by modifying the install.. bin script, and also the Jalview script.. cp install.. bin install.. bak.. cat install.. bak | sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" install.. sh install.. cp Jalview Jalview.. cat Jalview.. bak | sed "s/export LD_ASSUME_KERNEL/#xport LD_ASSUME_KERNEL/" Jalview.. sh Jalview.. In the application, open the preferences dialog window (Tools - Preferences) Open the tab labelled "Output" and then select which file formats to which you do not wish to append "/start-end".. Java Web Start version of Jalview fails with error Unable to Launch - because JAR resources in JNLP are not signed by same certificate.. This error (and others like it) is raised when an old version of the Jalview Webstart JNLP is being used to launch the latest version of the application (for instance, because you have created your own JNLP file in order to increase the memory available to Jalview).. To fix, first make sure that you are using the.. latest version of the Jalview JNLP file (right-click or apple-click to save this link to a file).. to launch jalview.. If you are using the latest version of the JNLP then you need to open the Java Web Start console panel, and flush any application caches and remove any old versions of Jalview listed in the application viewer.. To do this:.. Locate and open the java console on your system (in your control panel or systems settings, but may also be in the.. Utilities.. section of the Applications folder on OSX.. If you have access to a terminal, you can usually open the console with.. javaws -viewer.. Locate any jalview instances in your applications cache and remove them (usually, select the application and hit the delete or 'X' button).. Once you've cleared the cache, try to run the Jalview JNLP file again.. We publish Jalview using our own.. X.. 509 certificates.. When launching Jalview for the first time, you will be asked if you would like to accept the signing certificate.. Certificates are usually signed by the Barton Group (this information is in the technical details panel), and also include an expiry date.. If you use a version of Jalview with an expired certificate you will get a 'Signer's certificate has expired' warning, but if you press 'OK' or 'Accept', you should still be able to launch Jalview.. I downloaded the Jalview Installer for OSX but the install application won t run.. The OSX InstallAnywhere version of Jalview is downloaded as a ZIP archive (install.. zip) which is normally unpacked automatically to create an application called 'install' that you can run.. If nothing happens when you double click the application, then there are a few things that could go wrong.. Installer doesn't launch because it was unpacked with a third-party archive tool.. If you have chosen an alternative archive program for OSX to use to unpack ZIP files, then it probably didn't set the executable permissions for the application after it unpacked it.. The easiest solution is to.. right or option click the install.. zip that you downloaded.. , and choose '.. Open with - Archive Utility (10.. X).. ' (.. where X is the numeric version of OSX that you are running.. ); this will create a new 'install' application (probably called 'install 2') that you can now launch.. If using a different archiver doesn't work, or you are working from the console, then you need to delve into the installer's application directory.. Open the console,.. cd.. to the directory where the install application is located (probably ~/Downloads), and type:.. chmod u+x install.. app/Contents/MacOS/install open install.. app.. Permissions problems result in an error shown in the OSX Console window that reads something like.. ([0x0-0x6a86a8].. install[25620]) posix_spawn("/Users/jimp/install.. app/Contents/MacOS/install",.. ): Permission denied.. If you see anything else, paste it into the search box on.. http://issues.. to see if it has been reported.. Related bugs in the Jalview Issue Database:.. JAL-746..

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  • Title: Community | jalview.org
    Descriptive info: Who is the Jalview community ?.. Jalview is used for teaching and research all around the world; and, if you use Jalview, then we'd like you to be part of the community.. links page.. lists projects that use the web based version of Jalview - if yours isn't listed, or you use Jalview in other ways and would like to tell us, then we'd like to hear from you!.. Getting in touch.. There are plenty of ways you can keep in touch with other Jalview community members.. Our email lists have been running for a number of years, and you can use the RSS feed links to follow updates to the website.. If you're one of the twitterati, then you can tweet at.. @Jalview.. Email Lists.. Sign up to the news mailing list (.. jalview-announce.. ) to receive major announcements and notifications of  ...   join, register first on the.. jalview bug tracker.. and send the administrator a message.. Feeds.. Subscribe to the.. Desktop News.. feed to get updates on training courses, new releases and service interruptions.. jalview bug tracker feed.. to watch everything that goes on at the.. Jalview bug tracker.. Getting more involved.. If you want to help out with Jalview - whether you're a developer, a researcher, a teacher, or a student, then there are lots of things you can do.. Go to one of our.. training courses.. Sign up to.. and say hello.. Get an account on JIRA.. to report bugs, make feature requests, and find out what's being worked on at the moment.. Contact.. one of the current jalview team.. if you want to contribute code, fix bugs, write documentation and training material, or add a link to your work from the web site..

    Original link path: /community
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  • Title: Jalview-announce Info Page
    Descriptive info: Jalview-announce --.. About Jalview-announce.. English (USA).. Discussion list for users of the Jalview multiple alignment editor.. To see the collection of prior postings to the list, visit the.. Jalview-announce Archives.. Using Jalview-announce.. To post a message to all the list members, send email to.. jalview-announce@compbio.. dundee.. ac.. uk.. You can subscribe to the list, or change your existing subscription, in the sections below.. Subscribing to Jalview-announce.. Subscribe to Jalview-announce by filling out the following form.. You will be sent email requesting confirmation, to prevent others from gratuitously subscribing you.. This is a hidden list, which means that the list of members is available only to the list administrator.. Your email address:.. Your name (optional):.. You may enter a privacy password below.. This provides only mild security, but should prevent others from messing with  ...   You can always request a mail-back of your password when you edit your personal options.. Pick a password:.. Reenter password to confirm:.. Which language do you prefer to display your messages?.. English (USA).. Would you like to receive list mail batched in a daily digest?.. No.. Yes.. Jalview-announce Subscribers.. The subscribers list is only available to the list administrator.. ).. Enter your admin address and password to visit the subscribers list:.. Admin address:.. Password:.. To unsubscribe from Jalview-announce, get a password reminder, or change your subscription options enter your subscription email address:.. If you leave the field blank, you will be prompted for your email address.. Jalview-announce.. list run by.. jimp at compbio.. uk, t.. walsh at dundee.. Jalview-announce administrative interface.. (requires authorization).. Overview of all compbio.. uk mailing lists.. version 2.. 9..

    Original link path: /mailman/listinfo/jalview-announce
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