RT Journal Article
SR Electronic
T1 RAxML Grove: An empirical Phylogenetic Tree Database
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.10.05.463179
DO 10.1101/2021.10.05.463179
A1 Dimitri Höhler
A1 Wayne Pfeiffer
A1 Vassilios Ioannidis
A1 Heinz Stockinger
A1 Alexandros Stamatakis
YR 2021
UL http://biorxiv.org/content/early/2021/10/10/2021.10.05.463179.abstract
AB The assessment of novel phylogenetic models and inference methods is routinely being conducted via experiments on simulated as well as empirical data. When generating synthetic data it is often unclear how to set simulation parameters for the models and generate trees that appropriately reflect empirical model parameter distributions and tree shapes. As a solution, we present and make available a new database called ‘RAxML Grove’ currently comprising more than 60,000 inferred trees and respective model parameter estimates from fully anonymized empirical data sets that were analyzed using RAxML (1) and RAxML-NG (2) on two web servers. We also describe and make available two simple applications of RAxML Grove to exemplify its usage and highlight its utility for designing realistic simulation studies and analyzing empirical model parameter and tree shape distributions.RAxML Grove is freely available at https://github.com/angtft/RAxMLGrove.Competing Interest StatementThe authors have declared no competing interest.