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
Online Access:Get full text
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Summary: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.
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ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-017-3500-5