TreeFig

Converter that takes a figure of a phylogenetic tree and calculates a tree notation.

Requirements:

Requires the xmltodict and svg.path packages.

Testing:

There are some test .svg images in the test directory. Run the test script to generate their output files. bash test/run_tests.sh

Running:

I recommend using ImageMagick's suite of command-line tools to convert any screencap of a tree into a portable bitmap image.

Use the threshold function to render the image down to black and white; I recommend 50%, but you can tweak as needed. convert input_image -threshold 50% raw.pbm

Then use potrace to vectorize the image: potrace -s -k 0.8 -W 10 -H 10 -o my_tree.svg raw.pbm

Run the script with the vectorized file as the argument: python svg_converter.py my_tree.svg

The output files include my_tree_raw.svg, which contains the intermediate steps used in the calculation (this is good for debugging), my_tree.nex, and my_tree.nexml.

Caveats:

• As of Feb 28, 2016, the script only processes right-facing rectangular cladograms.
• It does not OCR the taxon names yet, but it does number them from the top down for easy matching later.
• The script does not handle very short nodes well.