Estimating Bayesian Phylogenetic Information Content
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Summary
This work focuses on measuring information about tree topology using marginal posterior distributions of tree topologies and shows that both the accuracy and the computational efficiency of topological information content estimation improve with use of the conditional clade distribution, which also allows topological Information content to be partitioned by clade.
- Type
- article
- Published
- 2016-05-06
- Cited by
- 42
- References
- 73
- Access
- Open access
- OpenAlex
- https://openalex.org/W2345412169
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:1011448
Keywords
Conditional entropy, Posterior probability, Entropy (arrow of time), Phylogenetic tree, Network topology
References
- Weighted relative entropy for phylogenetic tree based on 2-step Markov model.
- Information Theory: 1948-1998 - Guest Editorial
- The Phylogenetic Handbook: List of contributors
- Stochastic Models for Speciation Events in Phylogenetic trees
- Phylogenetic information and experimental design in molecular systematics
- A New Phylogenetic Diversity Measure Generalizing the Shannon Index and Its Application to Phyllostomid Bats
- Widespread horizontal transfer of mitochondrial genes in flowering plants
- Fast statistical tests for detecting heterotachy in protein evolution.
- Putting incertae sedis taxa in their place: a proposal for ten new families and three new genera in Sphaeropleales (Chlorophyceae, Chlorophyta)
- Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes
- BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
- CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
- A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases.
- IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
- New phylogenetic hypotheses for the core Chlorophyta based on chloroplast sequence data
- Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent.
- Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees
- Sequence length bounds for resolving a deep phylogenetic divergence.
- Automated Removal of Noisy Data in Phylogenomic Analyses
- Confidence in evolutionary trees from biological sequence data
Cited by
- The optimal rate for resolving a near-polytomy in a phylogeny.
- Evaluation of the information content of long-term wastewater characteristics data in relation to activated sludge model parameters.
- The Past Sure Is Tense: On Interpreting Phylogenetic Divergence Time Estimates
- GENOMIC PERSPECTIVES ON AMPHIBIAN EVOLUTION ACROSS MULTIPLE PHYLOGENETIC SCALES
- Mean and Variance of Phylogenetic Trees.
- Statistical Methods for Information Assessment and Data Compatibility with Applications
- What drives results in Bayesian morphological clock analyses?
- Assessing Combinability of Phylogenomic Data using Bayes Factors
- Measuring inferential importance of taxa using taxon influence indices
- Phylogeny, ancestors, and anagenesis in the hominin fossil record
- 19 dubious ways to compute the marginal likelihood of a phylogenetic tree topology.
- Identification and characterization of putative Aeromonas spp. T3SS effectors
- Phylogenetic Synecdoche Demonstrates Optimality of Subsampling and Improves Recovery of the Blaberoidea Phylogeny
- Model Choice, Missing Data and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships
- Order, please! Uncertainty in the ordinal-level classification of Chlorophyceae
- Information content for biological classifications
- Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees
- An Evolving View of Phylogenetic Support.
- Assessing support for Blaberoidea phylogeny suggests optimal locus quality
- Properties of Markov Chain Monte Carlo Performance across Many Empirical Alignments
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