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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Open accessAbstract
UNLABELLED: RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML). Low-level technical optimizations, a modification of the search algorithm, and the use of the GTR+CAT approximation as replacement for GTR+Gamma yield a program that is between 2.7 and 52 times faster than the previous version of RAxML. A large-scale performance comparison with GARLI, PHYML, IQPNNI and MrBayes on real data containing 1000 up to 6722 taxa shows that RAxML requires at least 5.6 times less main memory and yields better trees in similar times than the best competing program (GARLI) on datasets up to 2500 taxa. On datasets > or =4000 taxa it also runs 2-3 times faster than GARLI. RAxML has been parallelized with MPI to conduct parallel multiple bootstraps and inferences on distinct starting trees. The program has been used to compute ML trees on two of the largest alignments to date containing 25,057 (1463 bp) and 2182 (51,089 bp) taxa, respectively. AVAILABILITY: icwww.epfl.ch/~stamatak
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“A potential explanation could be that IQ-TREE uses NNI as its topological rearrangement mechanism (Nguyen et al. 2015), whereas RAxML and PhyML are both based on SPR (Stamatakis 2006; Guindon et al. 2010).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Stamatakis 2006
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MrBayes 3: Bayesian phylogenetic inference under mixed models
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Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr121 · Cited by 40,207
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Two new Later Stone Age sites from the Final Pleistocene in the Falémé Valley, eastern Senegal
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Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
Metadata
- Authors
- Stamatakis, A.
- Affiliations
- École Polytechnique Fédérale de Lausanne (CH)
- Corresponding author
- Stamatakis, Alexandros
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-08-23
- Volume
- 22
- Issue
- 21
- Pages
- 2688-2690
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2168696662
- Cited by
- 15,582
- References
- 12
- Citations by year
- 2026: 198 · 2025: 337 · 2024: 418 · 2023: 480 · 2022: 628 · 2021: 841 · 2020: 918 · 2019: 993 · 2018: 1019 · 2017: 1078 · 2016: 1245 · 2015: 1338 · 2014: 1714 · 2013: 1292 · 2012: 1075
- FWCI
- 82.83
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- cc-by-nc
- Locations
- Bioinformatics (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- reroDoc Digital Library (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
- Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
- 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 › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Diversity and Evolution
- Keywords
- maximum likelihood phylogenetic inference, large phylogenies, parallel computing, MPI, bootstrapping, software performance comparison, phylogenetics software
- MeSH terms
- Algorithms, Models, Genetic, Phylogeny, Sequence Homology, Nucleic Acid, Software, Species Specificity, Models, Statistical, Sequence Alignment, Conserved Sequence, Sequence Analysis, DNA, Evolution, Molecular
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