Hi Brooke, just continuing on with some questions on how to provide some simple effects to the tree utility:
An alternative to color striping is the ability to color subtrees. i am not sure how this is accomplished, perhaps some special markup symbol at the start and end of a section of tree to be colored. It might be easier/better to color the text rather than the tree. i don't know how difficult this would be. this would be incredibly useful . as in html <span style="color:#FF0000;">homSap</span> or <FONT COLOR=red>homSap</FONT> to make that text red. As it stands, the tree utility does not accept this, giving error message "Parser syntax error: illegal char '<' in phyloString" I suppose if the tree utility produced editable text in its pdf, color could be added after the tool returns its output. Maybe if the tree part and the text part were treated like adjacent html frames, it could work. the problem there is keeping the tree lines in register with mid-text lines. the attached jpeg shows a snippet of two large trees where i hacked a screenshot graphic to match text lines, and then a tree from a recent Science where they colored the subclades.
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