Molecular phylogenetics: principles and practice
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Summary
The major methods of phylogenetic analysis are reviewed, including parsimony, distance, likelihood and Bayesian methods, which discuss their strengths and weaknesses and provide guidance for their use.
- Type
- review
- Published
- 2012-03-28
- Cited by
- 736
- References
- 155
- OpenAlex
- https://openalex.org/W2071465766
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:1313627
Keywords
Phylogenetic tree, Biology, Phylogenetics, Evolutionary biology, Bayesian probability
References
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- Cases in which Parsimony or Compatibility Methods will be Positively Misleading
- MINIMUM MUTATION FITS TO A GIVEN TREE
- Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement
- Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model
- Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull
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- A draft genome of Yersinia pestis from victims of the Black Death
Cited by
- Genetic Population Structure and Cryptic Speciation of Ghost Shrimp (Neotrypaea californiensis) in North American West Coast Estuaries
- Analyzing Phylogenetic Trees with Timed and Probabilistic Model Checking: The Lactose Persistence Case Study
- Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences
- A Primer on Infectious Disease Bacterial Genomics
- Effects of Different Pretreatments of DNA Extraction from Dried Specimens of Ladybird Beetles (Coleoptera: Coccinellidae)
- A metaanalysis of bat phylogenetics and positive selection based on genomes and transcriptomes from 18 species
- Human Cultures are Primarily Adaptive at the Group Level (with comment)
- Reconciling gene family evolution and species evolution
- Using phylogenetic models to characterise natural selection from molecular data
- Genomic signals of selection within and phylogenetic relationships among Strongylocentrotid sea urchins
- A survey of Wolbachia, Spiroplasma and other bacteria in parthenogenetic and non-parthenogenetic phasmid (Phasmatodea) species
- Genetic history of salmonid fishes of the genus Oncorhynchus
- Probabilistic Models for Species Tree Inference and Orthology Analysis
- Immunoinformatics: towards an understanding of species-specific protein evolution using phylogenomics and network theory
- Molecular characterisation of microbial communities associated with live feed and fish larvae in a commercial fish farming system
- Morphological Diversity in Laminaria digitata: -different Species or different Phenotypes?
- Using phylogenetics and model selection to investigate the evolution of RNA genes in genomic alignments.
- Adaptive evolution in the Pseudomonas fluorescens Wsp signalling pathway : exploring the relationship between genetic cause and phenotypic effect
- The Forest for the Trees: Evaluating Molecular Phylogenies with an Emphasis on Higher-Level Decapoda
- Functional data analysis in phonetics
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