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NCHB: A method for constructing rooted phylogenetic networks from rooted triplets based on height function and
Hadi Poormohammadi1, Mohsen Sardari Zarchi2, Hossein Ghaneai2
1Department of Computer Engineering, Meybod University, Meybod, Iran; School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran.
Journal of Theoretical Biology
|January 9, 2020
Summary
A new heuristic method, NCHB, efficiently constructs optimal rooted phylogenetic networks from rooted triplets. NCHB minimizes reticulation nodes and network level, outperforming existing algorithms in evolutionary history modeling.
Area of Science:
- Computational Biology
- Evolutionary Biology
- Bioinformatics
Background:
- Phylogenetics models evolutionary history, with rooted phylogenetic networks handling non-tree-like events.
- Rooted triplets are crucial inputs for constructing these networks.
- Optimal rooted phylogenetic network construction from triplets is an NP-hard problem.
Purpose of the Study:
- Introduce NCHB, a novel heuristic method for efficient and optimal rooted phylogenetic network construction.
- Address the NP-hard challenge of building networks that encompass all given rooted triplets.
- Evaluate NCHB's performance against state-of-the-art algorithms.
Main Methods:
- Developed the NCHB heuristic method, incorporating height function and network binarization.
- Compared NCHB with LEV1ATHAN, SIMPLISTIC, and TripNet using biologically generated and software-generated triplet sets.
- Assessed performance based on minimizing reticulation nodes and network level.
Main Results:
- NCHB demonstrated superior performance over TripNet and SIMPLISTIC in constructing optimal networks.
- NCHB and LEV1ATHAN showed comparable results for level-1 networks.
- NCHB outputs closely matched optimal generated networks, outperforming other methods for higher-level networks.
Conclusions:
- NCHB offers an efficient and effective solution for constructing optimal rooted phylogenetic networks.
- The method innovatively utilizes height functions and binarization for improved network construction.
- NCHB advances the field of phylogenetics by providing a robust tool for modeling complex evolutionary histories.
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