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treeducken: An R package for simulating cophylogenetic systems
Author(s) -
Dismukes Wade,
Heath Tracy A.
Publication year - 2021
Publication title -
methods in ecology and evolution
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.425
H-Index - 105
ISSN - 2041-210X
DOI - 10.1111/2041-210x.13625
Subject(s) - approximate bayesian computation , r package , computer science , tree (set theory) , computation , host (biology) , bayesian probability , interface (matter) , machine learning , theoretical computer science , data mining , artificial intelligence , computational science , algorithm , parallel computing , inference , ecology , biology , mathematics , mathematical analysis , maximum bubble pressure method , bubble
Cophylogenetic methods describe discordance between non‐independent phylogenies. Simulation is necessary for testing cophylogenetic methods, but few simulators exist that are capable of generating data under explicit and biologically meaningful models. We present an R package, treeducken, for simulating host–symbiont evolution and gene‐tree–species‐tree evolution. treeducken provides a straightforward and reproducible interface for simulating cophylogenetic data. This allows easier performance testing of methods and has potential applications in machine learning (ML) and approximate Bayesian computation (ABC) approaches.