ReviewJournal of applied genetics2008
Statistical measures of uncertainty for branches in phylogenetic trees inferred from molecular sequences by using model-based methods.
Review in Journal of applied genetics, 2008. 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.
- Performance of tree-building methods using a morphological dataset and a well-supported Hexapoda phylogeny.PeerJ · 2024Article
- Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny.Nature communications · 2022Article
- Intra-species diversity ofFrontiers in microbiology · 2022Article
- Comparative genomics identifies potential virulence factors inVirulence · 2019Article
- Integrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia.Scientific reports · 2019Article
- Unveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for GenotypingFrontiers in microbiology · 2018Article
- treespace: Statistical exploration of landscapes of phylogenetic trees.Molecular ecology resources · 2017Article
- Complete chloroplast genome of Gracilaria firma (Gracilariaceae, Rhodophyta), with discussion on the use of chloroplast phylogenomics in the subclass Rhodymeniophycidae.BMC genomics · 2017Article
- A genetic analysis of taoyuan pig and its phylogenetic relationship to eurasian pig breeds.Asian-Australasian journal of animal sciences · 2015Article
- Molecular evolution of H9N2 avian influenza viruses in Israel.Virus genes · 2014Article
- A beginner's guide to phylogenetics.Microbial ecology · 2013Review
- Reconstructing the evolutionary history of transposable elements.Genome biology and evolution · 2013Article
- Bayesian models for comparative analysis integrating phylogenetic uncertainty.BMC evolutionary biology · 2012Article
- Article
- Statistics and truth in phylogenomics.Molecular biology and evolution · 2012Review
- Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes.Systematic biology · 2011Article
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1 author.
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Abstract
In recent years, the emphasis of theoretical work on phylogenetic inference has shifted from the development of new tree inference methods to the development of methods to measure the statistical support for the topologies. This paper reviews 3 approaches to assign support values to branches in trees obtained in the analysis of molecular sequences: the bootstrap, the Bayesian posterior probabilities for clades, and the interior branch tests. In some circumstances, these methods give different answers. It should not be surprising: their assumptions are different. Thus the interior branch tests assume that a given topology is true and only consider if a particular branch length is longer than zero. If a tree is incorrect, a wrong branch (a low bootstrap or Bayesian support may be an indication) may have a non-zero length. If the substitution model is oversimplified, the length of a branch may be overestimated, and the Bayesian support for the branch may be inflated. The bootstrap, on the other hand, approximates the variance of the data under the real model of sequence evolution, because it involves direct resampling from this data. Thus the discrepancy between the Bayesian support and the bootstrap support may signal model inaccuracy. In practical application, use of all 3 methods is recommended, and if discrepancies are observed, then a careful analysis of their potential origins should be made.
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