RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
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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. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.
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Chang was analyzed under its optimal PF-scheme using RAxML version 8.2.9, with support estimated using the rapid bootstrap option (100 replicates).
“Chang was analyzed under its optimal PF-scheme using RAxML version 8.2.9 [63], with support estimated using the rapid bootstrap option (100 replicates).”
From Improved Modeling of Compositional Heterogeneity Supports Sponges as Sister to All Other Animals (2017) · cites this paper as [63]
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- Authors
- Stamatakis, A.
- Affiliations
- Karlsruhe Institute of Technology (DE)
- Corresponding author
- Stamatakis, Alexandros
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2014-01-21
- Volume
- 30
- Issue
- 9
- Pages
- 1312-1313
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC3998144
- OpenAlex
- W2141052558
- Cited by
- 32,291
- References
- 11
- Citations by year
- 2026: 1771 · 2025: 2509 · 2024: 2952 · 2023: 2976 · 2022: 3436 · 2021: 4128 · 2020: 3907 · 2019: 3323 · 2018: 2686 · 2017: 2142 · 2016: 1486 · 2015: 750 · 2014: 182 · 2013: 4 · 2012: 1
- FWCI
- 622.94
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- Repository KITopen (Karlsruhe Institute of Technology) (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- KITopen
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Keywords
- RAxML, phylogenetic analysis, maximum likelihood estimation, large phylogenies, substitution models, memory reduction
- MeSH terms
- Models, Genetic, Phylogeny, Software, Likelihood Functions, High-Throughput Nucleotide Sequencing
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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