Coloring dendroscope files

How to programatically label phylogenies.

The need had arisen for the tips of a large phylogwny 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.

Usage

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
`--map-to-colors`
	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