treeducken: An R package for simulating cophylogenetic systems
Abstract 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, f...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2021-08-01
|
| Series: | Methods in Ecology and Evolution |
| Subjects: | |
| Online Access: | https://doi.org/10.1111/2041-210X.13625 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1825206689866973184 |
|---|---|
| author | Wade Dismukes Tracy A. Heath |
| author_facet | Wade Dismukes Tracy A. Heath |
| author_sort | Wade Dismukes |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-0d23d26f915841829a39a0f15add2c27 |
| institution | Kabale University |
| issn | 2041-210X |
| language | English |
| publishDate | 2021-08-01 |
| publisher | Wiley |
| record_format | Article |
| series | Methods in Ecology and Evolution |
| spelling | doaj-art-0d23d26f915841829a39a0f15add2c272025-02-07T06:21:05ZengWileyMethods in Ecology and Evolution2041-210X2021-08-011281358136410.1111/2041-210X.13625treeducken: An R package for simulating cophylogenetic systemsWade Dismukes0Tracy A. Heath1Department of Ecology, Evolution, and Organismal Biology Iowa State University Ames IA USADepartment of Ecology, Evolution, and Organismal Biology Iowa State University Ames IA USAAbstract 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.https://doi.org/10.1111/2041-210X.13625bioinformaticscommunity ecologyevolutionary biologymacroevolutionmolecular evolutionPhylogenetics |
| spellingShingle | Wade Dismukes Tracy A. Heath treeducken: An R package for simulating cophylogenetic systems Methods in Ecology and Evolution bioinformatics community ecology evolutionary biology macroevolution molecular evolution Phylogenetics |
| title | treeducken: An R package for simulating cophylogenetic systems |
| title_full | treeducken: An R package for simulating cophylogenetic systems |
| title_fullStr | treeducken: An R package for simulating cophylogenetic systems |
| title_full_unstemmed | treeducken: An R package for simulating cophylogenetic systems |
| title_short | treeducken: An R package for simulating cophylogenetic systems |
| title_sort | treeducken an r package for simulating cophylogenetic systems |
| topic | bioinformatics community ecology evolutionary biology macroevolution molecular evolution Phylogenetics |
| url | https://doi.org/10.1111/2041-210X.13625 |
| work_keys_str_mv | AT wadedismukes treeduckenanrpackageforsimulatingcophylogeneticsystems AT tracyaheath treeduckenanrpackageforsimulatingcophylogeneticsystems |