Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

RAxML Grove: An empirical Phylogenetic Tree Database

Dimitri Höhler, Wayne Pfeiffer, Vassilios Ioannidis, Heinz Stockinger, Alexandros Stamatakis
doi: https://doi.org/10.1101/2021.10.05.463179
Dimitri Höhler
1Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wayne Pfeiffer
3San Diego Supercomputer Center, University of California, San Diego, La Jolla, United States
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Vassilios Ioannidis
4SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Heinz Stockinger
4SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alexandros Stamatakis
1Computational Molecular Evolution group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
2Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: alexandros.stamatakis@h-its.org
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

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 Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted October 10, 2021.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
RAxML Grove: An empirical Phylogenetic Tree Database
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
RAxML Grove: An empirical Phylogenetic Tree Database
Dimitri Höhler, Wayne Pfeiffer, Vassilios Ioannidis, Heinz Stockinger, Alexandros Stamatakis
bioRxiv 2021.10.05.463179; doi: https://doi.org/10.1101/2021.10.05.463179
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
RAxML Grove: An empirical Phylogenetic Tree Database
Dimitri Höhler, Wayne Pfeiffer, Vassilios Ioannidis, Heinz Stockinger, Alexandros Stamatakis
bioRxiv 2021.10.05.463179; doi: https://doi.org/10.1101/2021.10.05.463179

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (4229)
  • Biochemistry (9108)
  • Bioengineering (6753)
  • Bioinformatics (23944)
  • Biophysics (12102)
  • Cancer Biology (9497)
  • Cell Biology (13742)
  • Clinical Trials (138)
  • Developmental Biology (7616)
  • Ecology (11662)
  • Epidemiology (2066)
  • Evolutionary Biology (15479)
  • Genetics (10620)
  • Genomics (14297)
  • Immunology (9467)
  • Microbiology (22793)
  • Molecular Biology (9078)
  • Neuroscience (48892)
  • Paleontology (355)
  • Pathology (1479)
  • Pharmacology and Toxicology (2565)
  • Physiology (3823)
  • Plant Biology (8309)
  • Scientific Communication and Education (1467)
  • Synthetic Biology (2290)
  • Systems Biology (6172)
  • Zoology (1297)