Version 12 It is now possible to add user plots from the command line using the JVM userplot option, e.g. art -Duserplot=/pathToFile/userPlot and for multiple plots this is comma separated art -Duserplot='/pathToFile/userPlot1,/pathToFile/userPlot2', it can also read the plots from URL's. Added support to be able to read BAM files to display read alignments. It uses picard (http://picard.sourceforge.net/) to read from the BAM file and so requires Artemis to be run with Java 1.6. See http://bamview.sourceforge.net/ for details. All graphs can now be configured to be plotted as line graphs or heat maps. Added support for BLAST tabular format (-m 8 option) and MSPcrunch format to plot scores. Added support for wiggle (variableStep/fixedStep) plots that can be displayed as histograms or heat maps. Added a new user plot file format with the first column specifying a base position. More configure options have been added to the graphs to enable configuration of the graph line style and size. GoTo directory option added to file manager to assist navigation. The database manager is cached between sessions (this can is on by default and can be switched off with -Ddatabase_manager_cache_off). There is an option under the File menu to clear this cache. A checkbox has been added to the window for adding ortholog/paralog links in the Gene Builder. If this is selected it adds links between existing ortholog/paralogs and the new ortholog/paralog. By default this is off. An option has been added to the database manager to display polypeptide domains in the feature display (as well as the protein map in the Gene Builder). An option has been added to the Run menu for doing a search of the Pfam database. Added an option to the Write menu for writing a combination of upstream + feature + downstream bases for selected features. Option added in the View->Filter Features menu to search for Duplicate Systematic Name Qualifier. Added options to set the minimum and maximum values of the plots. Transfer Annotation Tool (TAT) added to feature editor and Gene Builder. New graph popup menu option to show the values and average for a selected range. Added product_cv database option to define if the product is stored as a controlled vocabulary or as a feature property (featureprop).