What's New in the latest release (2.0.45)

1. A new look with cleaner buttons and slight rearrangement of the sequence window.

2. New tools: Golden Gate tool, Multigene Cre recombination, Calculator, Digest all open windows.

3. Updates to the ORF find function.

4. New alignment display- mouse over a base to see a popup of the abi trace. CDS features now show a translation in the alignment display.

5. Partial digests.

6. ABI files can be linked into sequence files by dragging the link icon from the ABI window onto a sequence window. When the sequence window is saved, the data from the abi file is saved with it in a text-encoded format so that the file can still be opened with a text editor.

What's New in the latest Alpha release (2.0.36)

Digest windows

  • Lane info button- mouse over the blue button in the upper right to get a listing of lane info
  • Digest lanes can be dragged from one digest window to another to generate a multi-lane gel
  • Digest lanes can be duplicated in a digest window by command-drag (ctrl-drag)

Circular maps

  • All new feature graphics
  • All texts (feature labels, enzyme names titles) can be moved with Command/Ctrl drag
  • All features can be moved with Command/Ctrl drag
  • Right-click to use a prototype of a formatting dialog

Linear maps

  • All new graphics
  • All texts (feature labels, enzyme names titles) can be moved with Command/Ctrl drag


  • Feature arrows and widths can be set (used in graphic maps)
  • Features can be hidden using the "Edit Features..." dialog

Transparent feature higlighting

  • Right click on the blue info button on the lower left corner of a sequence window
  • After configuring the transparency setting, you can mose-over the button to make overlapping features semi-transparent, allowing you to see where features overlap

GFF3 importing

  • For those dealing with the breakdown of Wormbase sequence export, you can now import GFF3 feature annotation files.
  • Steps: in the upper right corner of a genome browser window is a "File" menu
  • Chose export FASTA formatted file, save it and open in ApE
  • Chose export GFF3 annotations file, save it where you can find it again
  • In ApE, on the original FASTA file, chose "Features> Add Features from GFF3 File", then open the GFF3 file.
  • This will import all of the annotations.
  • You can also just open the GFF3 file from ApE's File menu, but it will use N's for the sequence.