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1. Bayesian phylogenetics
: methods, algorithms, and applications
by Kuo, Lynn, 1949 and Lewis, Paul O., 1961 and Chen, Ming-Hui, 1961
2014, Chapman & Hall/CRC mathematical and computational biology series, ISBN 1466500794, xxx, 365
Bayesian statistical decision theory | Phylogeny | Molecular genetics | Biometry
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2. Full Text Posterior Summarization in Bayesian Phylogenetics Using Tracer 1.7
by Rambaut, Andrew and Drummond, Alexei J and Xie, Dong and Baele, Guy and Suchard, Marc A
Systematic Biology, ISSN 1063-5157, 09/2018, Volume 67, Issue 5, pp. 901 - 904
Abstract Bayesian inference of phylogeny using Markov chain Monte Carlo (MCMC) plays a central role in understanding evolutionary history from molecular... 
Phylogenetics | Visualization | Bayesian inference | Markov chain Monte Carlo | EVOLUTIONARY BIOLOGY | visualization | MAXIMUM-LIKELIHOOD | phylogenetics | MODEL | PARAMETERS | INFERENCE | POPULATION-DYNAMICS | Software for Systematics and Evolution
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3. Full Text Model Selection in Phylogenetics
by Jack Sullivan and Paul Joyce
Annual Review of Ecology, Evolution, and Systematics, ISSN 1543-592X, 12/2005, Volume 36, Issue 1, pp. 445 - 466
Investigation into model selection has a long history in the statistical literature. As model-based approaches begin dominating systematic biology, increased... 
Datasets | Posadas | Phylogenetics | Evolution | Data models | Phylogeny | Nucleotides | Topology | Parametric models | Modeling | Likelihood ratio | AIC | Statistical phylogenetics | Decision theory | BIC | BOOTSTRAP SUPPORT | MAXIMUM-LIKELIHOOD-ESTIMATION | decision theory | EMPIRICAL-DATA | SPECIES GROUP | NUCLEOTIDE SUBSTITUTION | MITOCHONDRIAL-DNA | MOLECULAR PHYLOGENY | EVOLUTIONARY RATES | EVOLUTIONARY BIOLOGY | likelihood ratio | statistical phylogenetics | BAYESIAN-INFERENCE | SITE RATE VARIATION | Research | Analysis | Phylogeny (Botany) | Studies | Quantitative genetics | Nature | Data analysis | Taxonomy | Science | Biology | Deoxyribonucleic acid--DNA
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4. Full Text Molecular phylogenetics: Principles and practice
by Yang, Ziheng and Rannala, Bruce
Nature Reviews Genetics, ISSN 1471-0056, 05/2012, Volume 13, Issue 5, pp. 303 - 314
Phylogenies are important for addressing various biological questions such as relationships among species or genes, the origin and spread of viral infection... 
FOSSIL CALIBRATIONS | EVOLUTIONARY TREES | MAXIMUM-LIKELIHOOD | DNA-SEQUENCES | MIXTURE MODEL | ANCESTRAL POPULATION SIZES | GENETICS & HEREDITY | SPECIES DIVERGENCE TIMES | SUBSTITUTION MODELS | BAYESIAN-ESTIMATION | MULTIPLE SEQUENCE ALIGNMENT | Models, Biological | Base Sequence | Humans | Molecular Sequence Data | Female | Male | Software | Models, Statistical | Phylogeny | Usage | Cladistic analysis | Molecular genetics | Research | Nucleotide sequencing | Methods | DNA sequencing
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5. Full Text Bayesian phylogenetics with BEAUti and the BEAST 1.7
by Drummond, Alexei J and Suchard, Marc A and Xie, Dong and Rambaut, Andrew
Molecular Biology and Evolution, ISSN 0737-4038, 08/2012, Volume 29, Issue 8, pp. 1969 - 1973
Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and... 
coalescent theory | phylogenetics | evolution | Bayesian phylogenetics | molecular evolution | BIOCHEMISTRY & MOLECULAR BIOLOGY | SPECIES TREES | TIME | INFERENCE | CLOCKS | EVOLUTIONARY BIOLOGY | MODELS | GENETICS & HEREDITY | HISTORY | User-Computer Interface | Computational Biology - methods | Phenotype | Animals | DNA, Mitochondrial - genetics | Base Sequence | Bayes Theorem | Molecular Sequence Data | Finches - genetics | Software | Phylogeny
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6. Full Text The distinct distribution and phylogenetic characteristics of dengue virus serotypes/genotypes during the 2013 outbreak in Yunnan, China. Phylogenetic characteristics of 2013 dengue outbreak in Yunnan, China
by Wang, Binghui and Yang, Henglin and Feng, Yue and Zhou, Hongning and Dai, Jiejie and Hu, Yunzhang and Zhang, Li and Wang, Yajuan and Baloch, Zulqarnain and Xia, Xueshan
Infection, Genetics and Evolution, ISSN 1567-1348, 01/2016, Volume 37, pp. 1 - 7
Since 2000, sporadic imported cases of dengue fever were documented almost every year in Yunnan Province, China. Unexpectedly, a large-scale outbreak of dengue... 
Phylogenetic analysis | Imported infection | Outbreak | Bayesian analysis | Dengue | INFECTIOUS DISEASES | MOLECULAR EVOLUTION | TYPE-1 | EPIDEMIOLOGY | REVEALS | Dengue Virus - classification | Viral Envelope Proteins - genetics | Dengue - blood | Humans | Phylogeography | Dengue - epidemiology | Serogroup | Genotype | Male | China - epidemiology | Dengue - virology | Phylogeny | Dengue Virus - genetics | Disease Outbreaks | Bayes Theorem | Female | Medicine, Experimental | Medical research | Health aspects | Dengue viruses | Analysis
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7. Full Text Phylogenetic Methods in Biogeography
by Ronquist, Fredrik and Sanmartín, Isabel
Annual Review of Ecology, Evolution, and Systematics, ISSN 1543-592X, 12/2011, Volume 42, Issue 1, pp. 441 - 464
Phylogenetic approaches to biogeography are rapidly becoming more sophisticated. Four types of models are being explored in the literature: ( a ) diffusion... 
extinction | stochastic models | parsimony | maximum likelihood | dispersal | diversification | Bayesian inference | vicariance | speciation | Ecological modeling | Phylogeography | Parsimony | Biogeography | Phylogenetics | Evolution | Inference | Stochastic models | Modeling | Speciation | LONG-DISTANCE DISPERSAL | MOLECULAR EVOLUTION | GEOGRAPHIC RANGE EVOLUTION | HUMAN MITOCHONDRIAL-DNA | ISLAND BIOGEOGRAPHY | EVOLUTIONARY BIOLOGY | WEST WIND DRIFT | LIKELIHOOD FRAMEWORK | ECOLOGY | HISTORICAL BIOGEOGRAPHY | ANCESTRAL CHARACTER STATES | DISPERSAL-VICARIANCE ANALYSIS | Analysis | Methods
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8. Full Text High-Throughput Genomic Data in Systematics and Phylogenetics
by Emily Moriarty Lemmon and Alan R. Lemmon
Annual Review of Ecology, Evolution, and Systematics, ISSN 1543-592X, 1/2013, Volume 44, Issue 1, pp. 99 - 121
High-throughput genomic sequencing is rapidly changing the field of phylogenetics by decreasing the cost and increasing the quantity and rate of data... 
Polymerase chain reaction | Biological taxonomies | Taxa | Genomics in Ecology, Evolution and Ststematics Theme | Genomics | Phylogenetics | Genetic loci | Genomes | Phylogeny | Sequencing | Hybridity | Genomic partitioning | Hybrid enrichment | Targeted amplicon sequencing | High-throughput sequencing | Model selection | Locus selection | Transcriptome sequencing | Anchored phylogenomics | RAD sequencing | Next-generation sequencing | Ultraconserved element enrichment | Phylogeny estimation | Target enrichment | Phylogenomics | EUKARYOTIC GENOMES | ULTRACONSERVED ELEMENTS | ENRICHMENT STRATEGIES | transcriptome sequencing | targeted amplicon sequencing | phylogenomics | ultraconserved element enrichment | phylogeny estimation | MAXIMUM-LIKELIHOOD | next-generation sequencing | POPULATION GENOMICS | hybrid enrichment | anchored phylogenomics | model selection | MULTIPLE SEQUENCE ALIGNMENTS | ESTIMATING SPECIES TREES | locus selection | GENE TREES | EVOLUTIONARY BIOLOGY | BAYESIAN PHYLOGENETICS | target enrichment | ECOLOGY | genomic partitioning | high-throughput sequencing | Research | Nucleotide sequencing | DNA sequencing
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9. Full Text Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca)
by Colgan, D.J and Ponder, W.F and Beacham, E and Macaranas, J
Molecular Phylogenetics and Evolution, ISSN 1055-7903, 2007, Volume 42, Issue 3, pp. 717 - 737
Caenogastropoda is the dominant group of marine gastropods in terms of species numbers, diversity of habit and habitat and ecological importance. This paper... 
Multi-gene phylogeny | Ptenoglossa | Neogastropoda | Heteropoda | Cladistics | Maximum likelihood | Bayesian analysis | Architaenioglossa | Hypsogastropoda | CAMPANILE-SYMBOLICUM | cladistics | multi-gene phylogeny | BIOCHEMISTRY & MOLECULAR BIOLOGY | U2 SNRNA | MITOCHONDRIAL-DNA | INFERENCE | EVOLUTIONARY RATES | EVOLUTIONARY BIOLOGY | HISTONE H3 | SEQUENCE ALIGNMENT | maximum likelihood | GENETICS & HEREDITY | PARTIAL 28S RDNA | 18S RDNA | PROSOBRANCHIA | Likelihood Functions | Animals | RNA, Ribosomal, 18S - genetics | Snails - genetics | Bayes Theorem | RNA, Ribosomal, 16S - genetics | Electron Transport Complex IV - genetics | Phylogeny | Gastropoda - genetics | RNA, Ribosomal, 28S - genetics | Evolution, Molecular
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