News/Apollo 1.7.0 Released

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Version 1.7.0 of Apollo has just been released. You can access the updated Apollo page at

Changes in this version include

  • Added GFF3 support
  • Added program source filtering for reading off Chado databases
  • Lots of work on the ensj adapter to allow it to work better with recent ensembl schemas, handle ditags, give finer control of gene loading, increase speed of gene loading, bug fixes to history, cigar parsing in ensj layer, loading of contig features
  • Allow layout of display to be saved to / loaded from a file. Most useful for synteny where initial display set up can take time. The saved layout also includes the current base position and zoom factor, and on loading you can choose to use those.
  • Ability to edit settings for a type (new popup menu item in feature popup). The settings which can be edited are the glyph used for drawing the feature and the columns in the table displayed in the evidence panel.
  • New drawing glyph which shades exons darker or lighter depending on their phase (DrawablePhaseHighlightGeneFeatureSet). Also a version of that which uses straight lines to join exons rather than 'hats' (DrawablePhaseHighlightNoHatGeneFeatureSet)
  • Work on ensembl synteny adapter so it works with latest ensembl compara db schema, and basic support for allowing different alignment sets to be selected.
  • PureJDBCTransactionWriter added. This entailed some changes to other classes, but in almost every case the changes are 1. reverse compatible and 2. invisible to the end user.
  • Uses of Log4J for generating log files.

Plus many other changes. See the release notes for more.

We are hoping to cut releases on a more regular basis (after the year and a half long hiatus). So please let us know if you find any bugs and they will be addressed and put into a new release as soon as possible.

Posted to the GMOD News on 2008/01/11