A program to compute the soft Robinson–Foulds distance between phylogenetic networks

Background Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these rel...

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Published in:	BMC genomics Vol. 18; no. Suppl 2; p. 111
Main Authors:	Lu, Bingxin, Zhang, Louxin, Leong, Hon Wai
Format:	Journal Article
Language:	English
Published:	London BioMed Central 14.03.2017 Springer Nature B.V
Subjects:	Algorithms Animal Genetics and Genomics Animals Bioinformatics Biological Evolution Biomedical and Life Sciences C (programming language) Clusters Computational Biology - statistics & numerical data Computer programs Computer simulation Containment Culicidae - classification Culicidae - genetics Datasets Decomposition Genomics Life Sciences Microarrays Microbial Genetics and Genomics Models, Genetic Networks Phylogenetics Phylogeny Plant Genetics and Genomics Plant Proteins - genetics Poaceae - classification Poaceae - genetics Proteomics Reconstruction Rhizoctonia - classification Rhizoctonia - genetics RNA, Double-Stranded - genetics RNA, Fungal - genetics Software Trees (Soft) Robinson–Foulds distance Exponential-time algorithm Phylogenetic network Tree containment problem Cluster containment problem
ISSN:	1471-2164, 1471-2164
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Abstract	Background Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete. Results A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson–Foulds distance between phylogenetic networks. Conclusions Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson–Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data.
AbstractList	Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete.BACKGROUNDOver the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete.A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson-Foulds distance between phylogenetic networks.RESULTSA fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson-Foulds distance between phylogenetic networks.Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson-Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data.CONCLUSIONSTwo computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson-Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data. Background Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete. Results A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson–Foulds distance between phylogenetic networks. Conclusions Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson–Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data. Background Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete. Results A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson-Foulds distance between phylogenetic networks. Conclusions Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson-Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data. Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks, phylogenetic trees and clusters serve as the basis for reconstruction and comparison of phylogenetic networks. To understand these relationships, two problems are raised: the tree containment problem, which asks whether a phylogenetic tree is displayed in a phylogenetic network, and the cluster containment problem, which asks whether a cluster is represented at a node in a phylogenetic network. Both the problems are NP-complete. A fast exponential-time algorithm for the cluster containment problem on arbitrary networks is developed and implemented in C. The resulting program is further extended into a computer program for fast computation of the Soft Robinson-Foulds distance between phylogenetic networks. Two computer programs are developed for facilitating reconstruction and validation of phylogenetic network models in evolutionary and comparative genomics. Our simulation tests indicated that they are fast enough for use in practice. Additionally, the distribution of the Soft Robinson-Foulds distance between phylogenetic networks is demonstrated to be unlikely normal by our simulation data.
ArticleNumber	111
Author	Leong, Hon Wai Lu, Bingxin Zhang, Louxin
Author_xml	– sequence: 1 givenname: Bingxin surname: Lu fullname: Lu, Bingxin organization: Department of Computer Science, National University of Singapore – sequence: 2 givenname: Louxin surname: Zhang fullname: Zhang, Louxin email: matzlx@nus.edu.sg organization: Department of Mathematics, National University of Singapore – sequence: 3 givenname: Hon Wai surname: Leong fullname: Leong, Hon Wai organization: Department of Computer Science, National University of Singapore
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Keywords	(Soft) Robinson–Foulds distance Exponential-time algorithm Phylogenetic network Tree containment problem Cluster containment problem
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Snippet	Background Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic... Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic networks,... Background Over the past two decades, phylogenetic networks have been studied to model reticulate evolutionary events. The relationships among phylogenetic...
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SubjectTerms	Algorithms Animal Genetics and Genomics Animals Bioinformatics Biological Evolution Biomedical and Life Sciences C (programming language) Clusters Computational Biology - statistics & numerical data Computer programs Computer simulation Containment Culicidae - classification Culicidae - genetics Datasets Decomposition Genomics Life Sciences Microarrays Microbial Genetics and Genomics Models, Genetic Networks Phylogenetics Phylogeny Plant Genetics and Genomics Plant Proteins - genetics Poaceae - classification Poaceae - genetics Proteomics Reconstruction Rhizoctonia - classification Rhizoctonia - genetics RNA, Double-Stranded - genetics RNA, Fungal - genetics Software Trees
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Title	A program to compute the soft Robinson–Foulds distance between phylogenetic networks
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Volume	18
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