Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference.
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Summary
The phylogenetic trees inferred from data sets simulated under realistic, observed levels of heterogeneity for mammalian genes were reconstructed with accuracy comparable to those simulated with homogeneous nucleotide frequencies; the results hold for Neighbor-Joining, minimum evolution, maximum parsimony, and maximum-likelihood methods.
- Type
- article
- Published
- 2003-04-01
- Cited by
- 94
- References
- 67
- Access
- Open access
- OpenAlex
- https://openalex.org/W2100806401
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:16146632
Keywords
Phylogenetic tree, Biology, Evolutionary biology, Phylogenetic network, Phylogenetics
References
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- Nucleotide Composition Bias Affects Amino Acid Content in Proteins Coded by Animal Mitochondria
- Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used.
- Inferring phylogenies from DNA sequences of unequal base compositions.
- Compositional Bias May Affect Both DNA-Based and Protein-Based Phylogenetic Reconstructions
- Universal tree of life
- Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference.
- The Use of Tree Comparison Metrics
- Compositional statistics: An improvement of evolutionary parsimony and its application to deep branches in the tree of life
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- Performance of the relative-rate test under nonstationary models of nucleotide substitution.
- The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small.
- Phylogeny of the Lemuridae: Effects of Character and Taxon Sampling on Resolution of Species Relationships within Eulemur
- Estimation of evolutionary distances under stationary and nonstationary models of nucleotide substitution.
- Recovering a tree from the leaf colourations it generates under a Markov model
- Estimating the fraction of invariable codons with a capture-recapture method
Cited by
- Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences
- Systematics and historical biogeography of the genus Dugesia (platyhelminthes, Tricladida)
- Computational statistics in molecular phylogenetics
- Phylogeny of the Neuropterida: a first molecular approach
- Molecular diagnostics and phylogenetics of white grubs in sugarcane.
- Phylogenetic analyses of parasites in the new millennium.
- Structure, évolution et expression de gènes « chimériques » spécifiques des Primates
- Resolving the phylogeny of a speciose spider group, the family Linyphiidae (Araneae).
- Phylogeny, species delimitation and convergence in the South American bothriurid scorpion genus Brachistosternus Pocock 1893: Integrating morphology, nuclear and mitochondrial DNA.
- MySSP: Non-stationary evolutionary sequence simulation, including indels
- Genomic data support the hominoid slowdown and an Early Oligocene estimate for the hominoid-cercopithecoid divergence.
- Prokaryotic systematics in the genomics era
- Linking Fold, Function and Phylogeny: A Comparative Genomics View on Protein (Domain) Evolution
- Phylogenetic invariants for stationary base composition
- The Nature of Protein Domain Evolution: Shaping the Interaction Network
- Estimating divergence times in large molecular phylogenies
- Attributes and congruence of three molecular data sets: inferring phylogenies among Septoria-related species from woody perennial plants.
- Building trees of algae: some advances in phylogenetic and evolutionary analysis
- The “Naked Coral” Hypothesis Revisited – Evidence for and Against Scleractinian Monophyly
- Inverted replication of vertebrate mitochondria.
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