Using Robinson-Foulds supertrees in divide-and-conquer phylogeny estimation
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13015_2021_Article_189.pdf
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3.12 MB
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Author(s)
Yu, Xilin
Le, Thien
Christensen, Sarah A.
Molloy, Erin K.
Warnow, Tandy
Date Issued
June 28, 2021
Publisher
BioMed Central
Citation
Algorithms for Molecular Biology. 2021 Jun 28;16(1):12
Version
Final published version
Abstract
Abstract
One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. However, the construction of the Tree of Life is enormously computationally challenging, as all the current most accurate methods are either heuristics for NP-hard optimization problems or Bayesian MCMC methods that sample from tree space. One of the most promising approaches for improving scalability and accuracy for phylogeny estimation uses divide-and-conquer: a set of species is divided into overlapping subsets, trees are constructed on the subsets, and then merged together using a “supertree method”. Here, we present Exact-RFS-2, the first polynomial-time algorithm to find an optimal supertree of two trees, using the Robinson-Foulds Supertree (RFS) criterion (a major approach in supertree estimation that is related to maximum likelihood supertrees), and we prove that finding the RFS of three input trees is NP-hard. Exact-RFS-2 is available in open source form on Github at
https://github.com/yuxilin51/GreedyRFS
.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/s13015-021-00189-2
