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bioRxiv · 10.1101/2020.01.03.893743

NetCombin: An algorithm for optimal level-k network construction from triplets

Poormohammadi, H.·Sardari Zarchi, M.
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Abstract

Phylogenetic networks construction is one the most important challenge in phylogenetics. These networks can present complex non-treelike events such as gene flow, horizontal gene transfers, recombination or hybridizations. Among phylogenetic networks, rooted structures are commonly used to represent the evolutionary history of a species set, explicitly. Triplets are well known input for constructing the rooted networks. Obtaining an optimal rooted network that contains all given triplets is main problem in network construction. The optimality criteria include minimizing the level and the number of reticulation nodes. The complexity of this problem is known to be NP-hard. In this research, a new algorithm called Netcombin is introduced to construct an optimal network which is consistent with input triplets. The innovation of this algorithm is based on binarization and expanding processes. The binarization process innovatively uses a measure to construct a binary rooted tree T consistent with the maximum number of input triplets. Then T is expanded in an intellectual process by adding minimum number of edges to obtain final network with the minimum number of reticulation nodes. In order to evaluate the proposed algorithm, NetCombin is compared with four state of the art algorithms, RPNCH, NCHB, TripNet, and SIMPLISTIC. The experimental results on real data indicate that by considering the trade-off between speed and precision, the NetCombin outperforms the others. Author summaryHadi Poormohammadi got his PhD in Mathematics, Applied combinatorics from Shahid Beheshti University, Tehran, Iran in 2013. He is now working as an assistant professor at the Faculty of Computer Engineering, Meybod University. His research interests include Combinatorics, Graph theory and Bioinformatics. Mohsen Sardari Zarchi got his PhD in computer engineering, Artificial Intelligence from University of Isfahan in 2015. He is now working as an assistant professor at the Faculty of Computer Engineering, Meybod University. His research interests include Deep learning, Image processing, Artificial intelligence and Bioinformatics.

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Poormohammadi, H., Sardari Zarchi, M.. 2020-01-06. NetCombin: An algorithm for optimal level-k network construction from triplets. https://doi.org/10.1101/2020.01.03.893743

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