ArticleSystematic biology2017
Efficient Detection of Repeating Sites to Accelerate Phylogenetic Likelihood Calculations.
Article in Systematic biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Estimating Divergence Times and Diversification Rates with the Unresolved Fossilized Birth-Death Process.bioRxiv : the preprint server for biology · 2026Article
- Treeline Provides a Unified Strategy for Optimising Phylogenetic Trees Under Alternative Criteria.Molecular ecology resources · 2026Article
- Bit-reproducible parallel phylogenetic tree inference.Bioinformatics (Oxford, England) · 2026Article
- Bases-dependent Rapid Phylogenetic Clustering (Bd-RPC) enables precise and efficient phylogenetic estimation in viruses.Virus evolution · 2024Article
- DNA Sequences Are as Useful as Protein Sequences for Inferring Deep Phylogenies.Systematic biology · 2023Article
- Maximum likelihood pandemic-scale phylogenetics.Nature genetics · 2023Article
- A LASSO-based approach to sample sites for phylogenetic tree search.Bioinformatics (Oxford, England) · 2022Article
- Felsenstein Phylogenetic Likelihood.Journal of molecular evolution · 2021Article
- Harnessing machine learning to guide phylogenetic-tree search algorithms.Nature communications · 2021Article
- Phylogenetic tree building in the genomic age.Nature reviews. Genetics · 2020Review
- Improving the performance of Bayesian phylogenetic inference under relaxed clock models.BMC evolutionary biology · 2020Article
- ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models.Molecular biology and evolution · 2020Article
- RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference.Bioinformatics (Oxford, England) · 2019Article
- BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics.Systematic biology · 2019Article
- Molecular Analysis of Evolution and Origins of Cultivated Hawthorn (Frontiers in plant science · 2019Article
- Fast algorithms for computing phylogenetic divergence time.BMC bioinformatics · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The phylogenetic likelihood function (PLF) is the major computational bottleneck in several applications of evolutionary biology such as phylogenetic inference, species delimitation, model selection, and divergence times estimation. Given the alignment, a tree and the evolutionary model parameters, the likelihood function computes the conditional likelihood vectors for every node of the tree. Vector entries for which all input data are identical result in redundant likelihood operations which, in turn, yield identical conditional values. Such operations can be omitted for improving run-time and, using appropriate data structures, reducing memory usage. We present a fast, novel method for identifying and omitting such redundant operations in phylogenetic likelihood calculations, and assess the performance improvement and memory savings attained by our method. Using empirical and simulated data sets, we show that a prototype implementation of our method yields up to 12-fold speedups and uses up to 78% less memory than one of the fastest and most highly tuned implementations of the PLF currently available. Our method is generic and can seamlessly be integrated into any phylogenetic likelihood implementation. [Algorithms; maximum likelihood; phylogenetic likelihood function; phylogenetics].
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