TreeTime: Maximum-likelihood phylodynamic analysis
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Summary
TreeTime is presented, a Python based framework for phylodynamic analysis using an approximate Maximum Likelihood approach that can estimate ancestral states, infer evolution models, reroot trees to maximize temporal signals, estimate molecular clock phylogenies and population size histories.
- Type
- preprint
- Published
- 2017-06-21
- Cited by
- 1,138
- References
- 38
- Access
- Open access
- OpenAlex
- https://openalex.org/W2668254663
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:22041342
Keywords
Genome, Evolutionary biology, Python (programming language), Biology, Viral phylodynamics
References
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- Exploring the demographic history of DNA sequences using the generalized skyline plot.
- Estimation of branching dates among primates by molecular clocks of nuclear DNA which slowed down in Hominoidea
- Estimating the rate of evolution of the rate of molecular evolution.
- An examination of the constancy of the rate of molecular evolution
- Information, physics, and computation
- Relaxed Phylogenetics and Dating with Confidence
- Estimating divergence times in large phylogenetic trees.
- Structured coalescent processes on different time scales.
- Genetic Draft, Selective Interference, and Population Genetics of Rapid Adaptation
- The NumPy Array: A Structure for Efficient Numerical Computation
- Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies
Cited by
- Nextstrain: real-time tracking of pathogen evolution
- Real-Time Analysis and Visualization of Pathogen Sequence Data
- Network archaeology: phase transition in the recoverability of network history
- Full Genome Sequencing Reveals New Southern African Territories Genotypes Bringing Us Closer to Understanding True Variability of Foot-and-Mouth Disease Virus in Africa
- Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
- Bayesian inference of ancestral dates on bacterial phylogenetic trees
- Recent outbreaks of chikungunya virus (CHIKV) in Africa and Asia are driven by a variant carrying mutations associated with increased fitness for Aedes aegypti
- A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios
- Locally-adaptive Bayesian nonparametric inference for phylodynamics
- Efficient estimation of evolutionary rates by covariance aware regression
- Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing
- Recent advances in computational phylodynamics.
- Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia
- Comprehensive mapping of avian influenza polymerase adaptation to the human host
- Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season
- HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny
- Global Outbreaks and Origins of a Chikungunya Virus Variant Carrying Mutations Which May Increase Fitness for Aedes aegypti: Revelations from the 2016 Mandera, Kenya Outbreak
- Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010-2018.
- The ability of single genes vs full genomes to resolve time and space in outbreak analysis
- TreeCluster: Clustering biological sequences using phylogenetic trees
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