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Hillis suggested changes

I know that the branch lengths are arbitrary, but it would be good to be able to change the relative depth of clades on the tree. Now, I can adjust the horizontal length of the branches (the depth that a clade reaches back on the tree), but if I do this for one group, it changes all the others as well. What I want to do is change the horizontal length within one clade without changing the rest of the tree (within the constraints of the clade, of course...it will have limits based on the rest of the structure). Then I can show clades that diversify deep in the tree and clades that branch only toward the tips. I realize that this may be harder than is sounds, because right now, all the nodes of a particular level branch at the same horizontal position, and I'm asking that they be allowed to branch at different levels. If these levels need to be set up as discrete rather than continuous, it would still be good to be able to change the discrete level of a given node to move it deeper into the tree, where that was possible given the tree structure. If this isn't clear, let me know and I'll send an illustration of what I mean.
Especially when the node names can be used as terminal labels, it would be good to allow different labels to be represented by different sized fonts. Perhaps each label could be selected and the font size changed up or down?
If TJ is to be used for display, it would be nice to allow the addition of arrows or other symbols that could be used to point to or mark aspects of the tree. This might seem superfluous given the ability to mark clades, but there are other features of a tree that we might want to mark (e.g., a particular branch or taxon where something evolves). Also, if #4 below is difficult, then it would be important to be able to mark more than four groups or taxa.
I've already run out of group colors...can I mark more than four groups?
It would be very useful to have more control over which terminal labels are shown. I'd like to select a taxon name and delete it, or select a taxon and have the name displayed.
Can the colors of taxon names be controlled?
It would be great to be able to add labels to nodes from TJ, rather than having to modify the treefile (it can be a real pain to figure out where the labels of clades belong). I'd like to select a node and add a text label to it, and then save that information back to the file.
I think we talked about this one, but I'm not certain. Once I set up a tree (re-sized clades, marked groups, text re-sized, etc.), I liked to be able to save all those settings, so that I can re-open the tree to the same point.
Would it be possible to set up a treefile editor within the TJ? Right now, I don't know an easy way to edit these tree files. Changing the text files is not easy with a large treefile.

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Topic revision: r1 - 2006-01-11 - JamesSlack