FigTree re-coloring

The figtree-recolor.py script in this repo can be used to re-color the Nexus file that is saved by FigTree.

The process is slightly awkward, but it works.

Runs on (at least) Python 2.7.10 and 3.5

Caveats

This really is a hack. There are no tests for the code. I know almost nothing about the Nexus format or FigTree. This code may cease to work properly if the exact format of the Nexus output written by FigTree changes.

Andrew Rambaut says the "Import Colour Scheme" menu item in FigTree 1.4.3 will be working in a future version (Google group discussion).

Usage

Load your tree into FigTree. I think you may need to make some change to it (e.g., do a rotation at a node and then undo it) and then Save the file. FigTree will write out your tree in Nexus format.

You can then produce a new Nexus file with colored nodes using this script.

Specify your taxon colors

Create a text file with lines like

# This is a comment.
taxon1 #00FF00
taxon2 #FF00FF
taxon3 antique fuchsia

Lines are treated as comments if # is the first non-blank character on the line. Empty and whitespace-only lines are ignored.

Otherwise, lines must give a taxon name (no whitespace!) followed by a color. Colors are either specified as 6 hexadecimal digit RGB with a leading # (e.g., #00FF00 and #FF00FF above), or are given as a name (antique fuchsia above). To list the available names, see below.

By default, case will not be considered when matching taxa names against the first field of your color specification file. To change this, use the --matchCase option when calling figtree-recolor.py.

It is also possible for the first field of each line of the color specification file to be a regular expression to match taxa names against. In this case, you will need to run figtree-recolor.py with the --regex option. Regular expressions matches are not tied to the start of the taxon string, so remember to use ^ and $ if you want to tie your regular expression to one or both ends of the taxon name. Note that the first regular expression that matches a taxon will be the one whose color is used.

Create a new Nexus file

figtree-recolor.py writes a Nexus file on standard output. So you run it via:

$ figtree-recolor.py --nexusFile figtree.nexus --colorFile colors.txt > new.nexus

It can also read the Nexus from standard input:

$ figtree-recolor.py --colorFile colors.txt < figtree.nexus > new.nexus

If your Nexus file already has colors and you want to keep them (in the case where your color specification file doesn't indicate otherwise), you can preserve the original colors:

$ figtree-recolor.py --nexusFile figtree.nexus --colorFile colors.txt --preserveOriginalColors > new.nexus

The default is that all original colors will be stripped.

You can also specify a default color for taxa that are not given an explicit color in the color specification file. E.g.,

$ figtree-recolor.py --nexusFile figtree.nexus --colorFile colors.txt --defaultColor red > new.nexus

or

$ figtree-recolor.py --nexusFile figtree.nexus --colorFile colors.txt --defaultColor 0000FF > new.nexus

Note that if you use --preserveOriginalColors and a taxon has a pre-existing color (and is not named in the colors specification file), then the original color will be preserved (i.e., the default will not be applied).

If you use --colorFile /dev/null, all pre-existing colors will be removed (assuming you don't also use --preserveOriginalColors, of course).

View your colored tree

Once you've created a new Nexus file, go back into FigTree and open it.

Named colors

A list of the known color names (and their hex values) can be printed via:

$ figtree-recolor.py --listColors