Hi Shawn

> 1) Whenever a value other than "0" or "."  is entered in column 8 (holds
> "phase" data for CDS features), the feature does not display in the proper
> reading frame.  This only appears to affect the visuals..the feature
> information appears correct.  Editing the visual to produce the correct
> picture in the correct frame causes the coding region to shift incorrectly.
> Basically, if the visual is correct, the feature info is wrong, and visa
> versa.

I have not used Maker, but if you open the CDS feature to edit
(Edit->Selected Features in Editor) Artemis provides a codon_start (values
1,2 or 3) which can be used to define the frame the CDS appears in.

> 2) When I save/edit the gff3 (i.e. create or edit features) in Artemis, the
> file does not re-open properly--the gene models are lost.  In addition, once
> edited, the gff3 cannot be opened in Apollo either.

When you select File->Save As->GFF format there is an option in the save
dialog to flatten the gene model. Try unselecting that.


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