Hi Gershon -

This all makes perfect sense. There are a few minor patches needed in 
order to make this happen, and its not something I'm going to be able to 
do in the near future, since I'm working on getting the next release of 
Jalview out. That being said, this kind of project looks perfect for a 
google summer of code student (which I'm hoping Jalview will be 
participating in via 
http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2012). 
Do you know anyone who might be interested in taking on adding ancestral 
node/sequence support as a student project ?

Meanwhile, I've opened this improvement request on our issue tracker, 
and have uploaded your test files:
http://issues.jalview.org/browse/JAL-1055

Jim.

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