This is an implementation of tripVote: complete a set of gene trees to maximize the quartet score. The core algorithm is the Maximum Triplet Rooting (MTR) problem: Root a tree T according to a reference tree R such that the triplet score of T and R is maximized.

The algorithm and the code heavily depend on the tqDist software http://birc.au.dk/software/tqDist/. We would like to thank the authors for the code and algorithmic ideas.

Installation: using pip

pip install tripvote

Now you should be able to run the TripletVoting program. Type

tripVote_complete_trees.py -h

to learn how to use.

Below is an example (to run, you need to download the file incomplete.trees under folder test_cases of this repo to your machine):

tripVote_complete_trees.py -i incomplete.trees -o completed.trees

To root input trees with respect to rooted reference trees, use:

tripVote_root_trees.py -i unrooted.trees -r refTrees.trees -o rooted.trees

By default, the rooting command suppresses the old root if rerooting would otherwise leave a unary internal node. To keep the old root node and preserve that branch-length split exactly, add --preserve-old-root.

Notes:

• Older releases were distributed on PyPI as TripletVoting. Maintained releases are now distributed as tripvote.