Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2014 May 1;30(9):1312-3.
doi: 10.1093/bioinformatics/btu033. Epub 2014 Jan 21.

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis  1
Affiliations

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis. Bioinformatics. .

Abstract

Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community.

Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Aberer AJ, et al. Parallelized phylogenetic post-analysis on multi-core architectures. J. Comput. Sci. 2010;1:107–114.
    1. Berger SA, Stamatakis A. International Conference on Computer Systems and Applications (AICCSA), 2010 IEEE/ACS. New York, USA: IEEE; 2010. Accuracy of morphology-based phylogenetic fossil placement under maximum likelihood; pp. 1–9.
    1. Berger SA, et al. Performance, accuracy, and web server for evolutionary placement of short sequence reads under maximum likelihood. Syst. Biol. 2011;60:291–302. - PMC - PubMed
    1. Dao,D. et al. (2013) Automated plausibility analysis of large phyolgenies. Technical report. Karlsruhe Institute of Technology.
    1. Guindon S, et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of phyml 3.0. Syst. Biol. 2010;59:307–321. - PubMed

Publication types