Open AccessComparing the topology of phylogenetic network generators
Author(s) -
Remie Janssen,
Pengyu Liu
Publication year - 2021
Publication title -
journal of bioinformatics and computational biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.339
H-Index - 43
eISSN - 1757-6334
pISSN - 0219-7200
DOI - 10.1142/s0219720021400126
Subject(s) - phylogenetic network , phylogenetic tree , phylogenetics , computational phylogenetics , reticulate , prior probability , reticulate evolution , evolutionary biology , horizontal gene transfer , tree (set theory) , bayesian probability , topology (electrical circuits) , biology , computer science , artificial intelligence , mathematics , gene , genetics , paleontology , combinatorics
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive representation of evolutionary history compared to phylogenetic trees. Stochastic processes for generating random trees or networks are important tools in evolutionary analysis, especially in phylogeny reconstruction where they can be utilized for validation or serve as priors for Bayesian methods. However, as more network generators are developed, there is a lack of discussion or comparison for different generators. To bridge this gap, we compare a set of phylogenetic network generators by profiling topological summary statistics of the generated networks over the number of reticulations and comparing the topological profiles.