1. RunServiceApp, in general produces nexus files, not tree files.  Maybe I should add a method to
PhyloDataset to write a tree file.  Need a naming convention or something so we can associate a nexus file
and a tree file.  
	- raxml-bb: how do they handle results that consist of multiple trees, the bootstrap file for instance? In
	this case the "view" link shows the newick strings (see index.php, res=boots).

2. Let user specify outgroup before drawing tree.


3. See how to integrate with the cipres portal pages.

4. Newick: branch lens follow a colon.  Internal node names, if used, follow a closing parenthesis.  Raxml used node name as confidence score?  How to tell phy.fi to show internal node names or brlens?


Cipres portal notes
=====================================================================================================