Phylogenetic Bootstrapping under Resource Constraints: Higher Model Accuracy or more Replicates?
Explore this paper's citation graph
Summary
The trade-off, by means of the relative topological accuracy, is determined between investing resources into optimization of per-bootstrap replicate ML model parameters at the expense of computing less replicates versus superficial model parameter optimization for the sake of computing more replicates.
- Type
- article
- Published
- 2008-01-01
- Cited by
- 0
- References
- 21
- OpenAlex
- https://openalex.org/W49489258
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:15430933
Keywords
Bootstrapping (finance), Replicate, Computer science, Sampling (signal processing), Resource (disambiguation)
References
- Some probabilistic and statistical problems in the analysis of DNA sequences
- CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
- Phylogenomics and the reconstruction of the tree of life
- Comparison of phylogenetic trees
- A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach.
- Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes.
- Broad phylogenomic sampling improves resolution of the animal tree of life
- Evolutionary trees from DNA sequences: A maximum likelihood approach
- Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion
- Does choice in model selection affect maximum likelihood analysis?
- Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences.
- Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
- A rapid bootstrap algorithm for the RAxML Web servers.
- Phylogenomics: the beginning of incongruence?
- RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
- Phylogenetic models of rate heterogeneity: a high performance computing perspective
- Bootstrap Methods: Another Look at the Jackknife
- Comparison of weighted labelled trees
Cited by
No citing papers recorded for this paper.
Related papers
- Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method
- Mixed Integer Linear Programming for Maximum-Parsimony Phylogeny Inference
- Optimization Problems in Data Mining
- Random search for hyper-parameter optimization
- The Update Complexity of Selection and Related Problems
- A Simple Approach for Finding the Globally Optimal Bayesian Network Structure
- The Y-Test: Fairly Comparing Experimental Setups with Unequal Effort
- Simulation-Based Optimization of Virtual Nesting Controls for Network Revenue Management