larsga / sprake

Visualizer for phylogenetic trees

sprake

Sprake is a Python 3 command-line tool and API for rendering phylogenetic trees.

By default it will just render a straight black-and-white tree, but if you have a CSV file with metadata about the nodes you can use style rules to change formatting of nodes based on their properties.

Supported output formats: PNG, SVG, and PDF.

Example output

Simple usage

python3 sprake-cli.py tree.nwk --format PDF

This will produce the output in tree.pdf.

To use style rules:

python3 sprake-cli.py tree.nwk --format PDF --data tree.csv --style tree.style

To run the examples yourself, run:

python3 sprake-cli.py examples/scer-x-skud.nwk --data examples/scer-x-skud.csv \\
  --style examples/scer-x-skud.style --format SVG

Examples of style

Let's say tree.csv looks like this:

ID	POF
A	True
B	False

If you then declare the following in tree.style:

POF=True,dotcolor=#FF0000
POF=False,dotcolor=#0000FF

Then node A will get a red dot next to its name, and node B will get a blue dot.

You can also change text color, line color, line thickness, and so on. Example:

culture=1, textcolor=#b3059e, linecolor=#b3059e, linewidth=2
culture=2, textcolor=#4dab4d, linecolor=#4dab4d, linewidth=2

(The file format for style rules is going to change. The syntax above is temporary while a better format is being designed.)

Output formats

Format	Requirements	Status
PDF	fpdf2	Quite good
SVG	-	Good
PNG	PIL	Not working