Phylogenies: Adding Colors

Question

[Lee Katz]

Hi Biostars, I am wondering how to decorate a tree properly on the command line. I need to add colors to specific nodes that I have in a separate spreadsheet. I am able to do that with Bio::TreeIO and the other BioPerl modules. However, how do I add colors? Looking at Nexus files generated from FigTree, it looks possible. I am just wondering how to implement it in BioPerl.

While we're on the subject, how do we do other things like adding bold, underline, italics, font changes, etc? Thank you!

edit I just want to bump this up in case this question got pushed down too far. I'm looking forward to making pretty trees!

Answer 1

[Josh Herr]

Hi Lee Katz,

I do most of my phylogenetic tree editing in FigTree, which I like a lot, and do any pre-publication cleaning in Illustrator. As far as command line, I have let go of any BioPerl I was using, and now when I want to generate phylogenetic trees and place accents on them I use BioPython and particularly the ETE package (which now has nice integration with ipython-notebook).

[Lee Katz]

So if I understand correctly, your strategy is to simply make a PDF out of a given tree? Not to apply color and font attributes to a tree file?

[youngcsong]

I don't think that's what he meant. You can still add color/font attributes with Illustrator. As a matter of fact, in my opinion, Illustrator works much more efficiently in aesthetics perspective than using command line tools. I usually edit my trees (and other things, such as graphics file generated with R), to the extent that the actual data represented by the image is not distorted.

[Josh Herr]

+1, yes, thanks for clarifying my post youngcsong