(Q37997899)

26 August 2017

title

Molecular phylogenetics: principles and practice (English)

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26 August 2017

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Ziheng Yang

1

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26 August 2017

Bruce Rannala

series ordinal

2

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26 August 2017

language of work or name

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28 March 2012

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26 August 2017

published in

Nature Reviews Genetics

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26 August 2017

volume

13

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26 August 2017

issue

5

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26 August 2017

page(s)

303-314

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Phylogenetic relationships within cation transporter families of Arabidopsis

26 August 2017

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Phylogenetic analysis. Models and estimation procedures

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Minimum Mutation Fits to a Given Tree

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Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods

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Among-site rate variation and its impact on phylogenetic analyses

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Acoelomorph flatworms are deuterostomes related to Xenoturbella

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Systematic error in seed plant phylogenomics

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Evolutionary trees from DNA sequences: A maximum likelihood approach

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Phylogenetic analysis using parsimony and likelihood methods

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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

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Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods

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Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution

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Phylogenetic methods come of age: testing hypotheses in an evolutionary context

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Molecular phylogenetics: state-of-the-art methods for looking into the past

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Relaxed phylogenetics and dating with confidence

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Confidence Limits on Phylogenies: an Approach using the Bootstrap

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Bootstrap confidence levels for phylogenetic trees

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First-order correct bootstrap support adjustments for splits that allow hypothesis testing when using maximum likelihood estimation.

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Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

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Polytomies and Bayesian phylogenetic inference

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Branch-length prior influences Bayesian posterior probability of phylogeny.

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Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models

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When trees grow too long: investigating the causes of highly inaccurate bayesian branch-length estimates.

21 January 2018

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Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference.

21 January 2018

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Many-core algorithms for statistical phylogenetics

21 January 2018

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FPGA Acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods

21 January 2018

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The supermatrix approach to systematics

21 January 2018

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Maximum-Likelihood Models for Combined Analyses of Multiple Sequence Data

21 January 2018

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Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences

21 January 2018

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A likelihood look at the supermatrix-supertree controversy

21 January 2018

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SDM: a fast distance-based approach for (super) tree building in phylogenomics

21 January 2018

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Phylogenetic inference under varying proportions of indel-induced alignment gaps

21 January 2018

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Mutation-selection models of coding sequence evolution with site-heterogeneous amino acid fitness profiles

21 January 2018

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A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data

21 January 2018

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Rooting the eutherian tree: the power and pitfalls of phylogenomics

21 January 2018

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Testing congruence in phylogenomic analysis

21 January 2018

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CLUSTAL: a package for performing multiple sequence alignment on a microcomputer

21 January 2018

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

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An algorithm for progressive multiple alignment of sequences with insertions

21 January 2018

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Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

21 January 2018

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An evolutionary model for maximum likelihood alignment of DNA sequences

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Recursions for statistical multiple alignment

21 January 2018

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Joint Bayesian Estimation of Alignment and Phylogeny

21 January 2018

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Bayesian coestimation of phylogeny and sequence alignment

21 January 2018

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Estimating the rate of evolution of the rate of molecular evolution

21 January 2018

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Performance of a divergence time estimation method under a probabilistic model of rate evolution

21 January 2018

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Inferring speciation times under an episodic molecular clock

21 January 2018

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Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds

21 January 2018

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The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times

21 January 2018

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Using the fossil record to estimate the age of the last common ancestor of extant primates

21 January 2018

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Dating primate divergences through an integrated analysis of palaeontological and molecular data

21 January 2018

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Bayesian phylogeography finds its roots

21 January 2018

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Phylogeography takes a relaxed random walk in continuous space and time

21 January 2018

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Divergence time and population size in the lineage leading to modern humans

21 January 2018

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Isolation with migration models for more than two populations

21 January 2018

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Delimiting species without monophyletic gene trees

21 January 2018

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Bayesian species delimitation using multilocus sequence data

21 January 2018

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Genomic DNA sequences from mastodon and woolly mammoth reveal deep speciation of forest and savanna elephants

21 January 2018

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A draft genome of Yersinia pestis from victims of the Black Death

21 January 2018

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Genetic evidence for complex speciation of humans and chimpanzees

21 January 2018

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The effect of gene flow on the coalescent time in the human-chimpanzee ancestral population.

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A new approach to estimate parameters of speciation models with application to apes

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Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model

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21 January 2018

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A likelihood ratio test of speciation with gene flow using genomic sequence data

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Genetic history of an archaic hominin group from Denisova Cave in Siberia

21 January 2018

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The position of gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics

21 January 2018

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21 January 2018

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HyPhy: hypothesis testing using phylogenies

21 January 2018

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PAML 4: phylogenetic analysis by maximum likelihood

21 January 2018

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Computing Bayes factors using thermodynamic integration.

21 January 2018

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Improving marginal likelihood estimation for Bayesian phylogenetic model selection

21 January 2018

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Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees

21 January 2018

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Evolution of Protein Molecules

21 January 2018

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PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES

31 March 2020

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Evolutionary Divergence and Convergence in Proteins

31 March 2020

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Phylogenetic Tree Construction Using Markov Chain Monte Carlo

31 March 2020

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Confidence Limits on Phylogenies: an Approach using the Bootstrap

31 March 2020

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Robustness of compound Dirichlet priors for Bayesian inference of branch lengths.

31 March 2020

1 reference

Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites

31 March 2020

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12 December 2020

Estimating the pattern of nucleotide substitution

1 reference

12 December 2020

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci

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12 December 2020

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data

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12 December 2020

The neighbor-joining method: a new method for reconstructing phylogenetic trees

1 reference

12 December 2020

Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene

1 reference

12 December 2020

Systematic bias in phylogenetic analysis: is the Strepsiptera problem solved?

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12 December 2020

Interior-branch and bootstrap tests of phylogenetic trees.

1 reference

12 December 2020

Identifiers

DOI

10.1038/NRG3186

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26 August 2017

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