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 TripletVotingNow you should be able to run the TripletVoting program. Type
tripVote_complete_trees.py -hto 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