Ultimately, the previous poster is correct that you will at some point end up importing your tree into a vector graphics program for final annotation. To amplify that point, most of the time you only want to have bootstrap values for a few major branches above a certain threshold. That number is almost always small enough that it's easiest to put those numbers in by hand in your drawing program.
That being said, Archaeopteryx has a great deal of functionality for editing trees, and there is some latitude for how bootstrap numbers are displayed.
To get an idea of what you can do with Archaeopteryx, see the tutorial Visualization of Phylogenetic Trees.
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brian.fristensky
