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

RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference

View ORCID ProfileAlexey M. Kozlov, View ORCID ProfileDiego Darriba, View ORCID ProfileTomáš Flouri, View ORCID ProfileBenoit Morel, View ORCID ProfileAlexandros Stamatakis
doi: https://doi.org/10.1101/447110
Alexey M. Kozlov
1Scientific Computing 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
  • ORCID record for Alexey M. Kozlov
  • For correspondence: alexey.kozlov@h-its.org
Diego Darriba
1Scientific Computing 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
  • ORCID record for Diego Darriba
Tomáš Flouri
1Scientific Computing 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
  • ORCID record for Tomáš Flouri
Benoit Morel
1Scientific Computing 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
  • ORCID record for Benoit Morel
Alexandros Stamatakis
1Scientific Computing Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
2Institute of 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
  • ORCID record for Alexandros Stamatakis
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Motivation Phylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine. Finding the optimal tree under the popular maximum like-lihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.

Results We present RAxML-NG, a from scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML- NG offers improved accuracy, flexibility, speed, scalability, and usability compared to RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and a the recently introduced transfer bootstrap support metric.

Availability The code is available under GNU GPL at https://github.com/amkozlov/raxml-ng.RAxML-NG web service (maintained by Vital- IT) is available at https://raxml-ng.vital-it.ch/.

Contact alexey.kozlov{at}h-its.org

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 4.0 International license.
Back to top
PreviousNext
Posted April 23, 2019.
Download PDF

Supplementary Material

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-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference
(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-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference
Alexey M. Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, Alexandros Stamatakis
bioRxiv 447110; doi: https://doi.org/10.1101/447110
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference
Alexey M. Kozlov, Diego Darriba, Tomáš Flouri, Benoit Morel, Alexandros Stamatakis
bioRxiv 447110; doi: https://doi.org/10.1101/447110

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 (4087)
  • Biochemistry (8768)
  • Bioengineering (6481)
  • Bioinformatics (23348)
  • Biophysics (11753)
  • Cancer Biology (9150)
  • Cell Biology (13256)
  • Clinical Trials (138)
  • Developmental Biology (7417)
  • Ecology (11371)
  • Epidemiology (2066)
  • Evolutionary Biology (15091)
  • Genetics (10402)
  • Genomics (14012)
  • Immunology (9122)
  • Microbiology (22050)
  • Molecular Biology (8780)
  • Neuroscience (47381)
  • Paleontology (350)
  • Pathology (1420)
  • Pharmacology and Toxicology (2482)
  • Physiology (3705)
  • Plant Biology (8054)
  • Scientific Communication and Education (1431)
  • Synthetic Biology (2209)
  • Systems Biology (6016)
  • Zoology (1250)