Using RAxML to infer phylogenies
Abstract
Inference of phylogenetic trees under the maximum likelihood (ML) criterion represents a routine task in biological data analysis. In this unit we describe how to plan analyses and use Randomized Accelerated Maximum Likelihood (RAxML) for phylogenetic inferences under ML, how to infer support values using the standard bootstrap procedure as well as other statistical measures, and how to conduct post‐analyses on collections/sets of phylogenetic trees including statistical significance tests and consensus tree methods. We also discuss what measures can be taken and what further analyses can be conducted when relationships in the inferred tree exhibit “low” support. © 2015 by John Wiley & Sons, Inc.
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A possible explanation for RAxML/ExaML not yielding highest likelihood scores is that, due to its 'lazy SPR' heuristic, RAxML might report trees that are not optimal in terms of strict NNI or SPR rearrangement.
“One possible explanation is that, due to its “lazy SPR” heuristic, RAxML might report trees that are not optimal in terms of strict NNI or SPR rearrangement (Stamatakis 2015).”
From Evaluating fast maximum likelihood-based phylogenetic programs using empirical phylogenomic data sets (2018) · cites this paper as Stamatakis 2015
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- Authors
- Stamatakis, A.
- Affiliations
- Karlsruhe Institute of Technology (DE)
- Corresponding author
- Stamatakis, Alexandros
- Venue
- Current Protocols in Bioinformatics
- Publisher
- Wiley
- Published
- 2015-09
- Volume
- 51
- Issue
- 1
- Pages
- 6.14.1-6.14.14
- ISSN
- 1934-3396 (ISSN-L)
- 1934-340X
- OpenAlex
- W1782752371
- Cited by
- 243
- References
- 31
- Citations by year
- 2026: 10 · 2025: 18 · 2024: 25 · 2023: 22 · 2022: 21 · 2021: 26 · 2020: 44 · 2019: 27 · 2018: 31 · 2017: 13 · 2016: 4 · 2015: 1 · 2012: 1
- FWCI
- 7.09
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Current Protocols in Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- 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 › Genetics › Genetic diversity and population structure
- Keywords
- RAxML, phylogenetic inference, maximum likelihood estimation, consensus trees, statistical significance tests, phylogenomics
- MeSH terms
- Computer Simulation, Data Interpretation, Statistical, Genetics, Population, Models, Genetic, Phylogeny, Models, Statistical, Likelihood Functions
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