Coloring dendroscope files

How to programatically label phylogenies.

The need had arisen for the tips of a large phylogeny to be labelled in a systematic way. Rather than "point and click" within Dendroscope, this script takes a .den/dendro file and colors the tips according to a "color description" file. This is a simple csv file with taxa labels and a corresponding color. The color may either be an RGB triplet or a scalar value which will be mapped to a pallete.


color-dendro.rb [options] CLRFILE TREEFILE1 [...]

where the options are:

-h, --help Display this screen
-m, --default-color STR
 The default color nodes will be given
 The coloring instructions give a float value which will be mapped to a color
--save STR Name output files according this template
-o, --overwrite
 Overwrite pre-existing files


The color palette / spectrum code is very primitive and should be improved.


Thanks to Richard Myers for his original script which this is based on.