LS³: A Method for Improving Phylogenomic Inferences When Evolutionary Rates Are Heterogeneous among Taxa
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Summary
An objective criterion for assessing lineage evolutionary rate heterogeneity among predefined lineages is defined: the result of a likelihood ratio test between a model in which the lineages evolve at the same rate and a models in which different lineage rates are allowed.
- Type
- article
- Published
- 2016-02-23
- Cited by
- 14
- References
- 48
- Access
- Open access
- OpenAlex
- https://openalex.org/W2286898890
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:205211156
Keywords
Biology, Phylogenetic tree, Lineage (genetic), Inference, Evolutionary biology
References
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- Cases in which Parsimony or Compatibility Methods will be Positively Misleading
- Perceptions and Experiences of Research Participants on Gender-Based Violence Community Based Survey: Implications for Ethical Guidelines
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- Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data
- Inferring ancient divergences requires genes with strong phylogenetic signals
- Evidence for a clade of nematodes, arthropods and other moulting animals
- OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
- Automated Removal of Noisy Data in Phylogenomic Analyses
- Long Branch Effects Distort Maximum Likelihood Phylogenies in Simulations Despite Selection of the Correct Model
- Molecular phylogenetics: principles and practice
- The guinea-pig is not a rodent
- A review of long‐branch attraction
- Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants
- Evolutionary trees from DNA sequences: A maximum likelihood approach
- A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
- Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics.
- PAML 4: phylogenetic analysis by maximum likelihood.
- Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa.
Cited by
- Negative correlation between rates of molecular evolution and flowering cycles in temperate woody bamboos revealed by plastid phylogenomics
- The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
- Testing cospeciation through large-scale cophylogenetic studies.
- Comprehensive phylogeny of acariform mites (Acariformes) provides insights on the origin of the four-legged mites (Eriophyoidea), a long branch.
- LSX: automated reduction of gene-specific lineage evolutionary rate heterogeneity for multi-gene phylogeny inference
- Back to the roots: Reducing evolutionary rate heterogeneity among sequences gives support for the early morphological hypothesis of the root of Siluriformes (Teleostei: Ostariophysi).
- Sequence selection by FitSS4ASR alleviates ancestral sequence reconstruction as exemplified for geranylgeranylglyceryl phosphate synthase
- PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies
- Phylogenetic tree building in the genomic age
- Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)
- Phylogenomics
- Emergence of a novel genotype of class II New Castle Disease virus in North Eastern States of India.
- Identifying and addressing methodological incongruence in phylogenomics: A review
- Exploring systematic biases, rooting methods and morphological evidence to unravel the evolutionary history of the genus Ficus (Moraceae)
- Sources of Error and Incongruence in Phylogenomic Analyses
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