(Q21146068)

17 August 2022

1

Alexei J Drummond

Alexei J

Drummond

1 reference

17 August 2022

2

Simon Y W

Ho

Simon Y W Ho

1 reference

17 August 2022

Matthew J Phillips

3

Matthew J

Phillips

1 reference

16683862

Rooting a phylogenetic tree with nonreversible substitution models

17 August 2022

language of work or name

English

0 references

publication date

May 2006

0 references

published in

PLOS Biology

0 references

volume

4

0 references

issue

5

0 references

page(s)

e88

0 references

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

The molecular population genetics of HIV-1 group O

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Long term trends in the evolution of H(3) HA1 human influenza type A

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Body size, metabolic rate, generation time, and the molecular clock

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

MRBAYES: Bayesian inference of phylogenetic trees

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Evolutionary trees from DNA sequences: A maximum likelihood approach

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Bayesian coalescent inference of past population dynamics from molecular sequences

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Genome-scale phylogeny and the detection of systematic biases

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Estimation of primate speciation dates using local molecular clocks

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Timing the ancestor of the HIV-1 pandemic strains

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

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

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Vagaries of the molecular clock

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Genome-scale approaches to resolving incongruence in molecular phylogenies

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Divergence time and evolutionary rate estimation with multilocus data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach

7 April 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

7 April 2017

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.0040088

Estimating the rate of evolution of the rate of molecular evolution

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Phylogenomics of eukaryotes: impact of missing data on large alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Comparative analyses of multi-species sequences from targeted genomic regions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

The reconstructed evolutionary process

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Phylogenetic test of the molecular clock and linearized trees

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Rates of DNA sequence evolution differ between taxonomic groups

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

The general stochastic model of nucleotide substitution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Tracing the decay of the historical signal in biological sequence data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Precision of molecular time estimates

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Ecological and immunological determinants of influenza evolution.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Model misspecification and probabilistic tests of topology: evidence from empirical data sets

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

An integrated framework for the inference of viral population history from reconstructed genealogies.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Genealogical inference from microsatellite data

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Selection-driven evolution of emergent dengue virus

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Estimating divergence dates from molecular sequences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Nuclear gene sequences provide evidence for the monophyly of australidelphian marsupials

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Evolutionary Divergence and Convergence in Proteins

30 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.0040088

A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.0040088

Estimating divergence times in the presence of an overdispersed molecular clock

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.0040088

Molecular dates for the "cambrian explosion": the influence of prior assumptions.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Branch-length prior influences Bayesian posterior probability of phylogeny.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Closing the gap between rocks and clocks

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

The importance of proper model assumption in bayesian phylogenetics.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Dating the monocot-dicot divergence and the origin of core eudicots using whole chloroplast genomes

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Effects of Models of Rate Evolution on Estimation of Divergence Dates with Special Reference to the Metazoan 18S Ribosomal RNA Phylogeny

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Inferring the root of a phylogenetic tree

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Mass survival of birds across the Cretaceous-Tertiary boundary: molecular evidence

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Determinants of rate variation in mammalian DNA sequence evolution

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1395354

Measurably evolving populations

29 November 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.0040088

7 January 2021

Equation of State Calculations by Fast Computing Machines

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.0040088

7 January 2021

Monte Carlo sampling methods using Markov chains and their applications

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.0040088

7 January 2021

On the Genealogy of Large Populations

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.0040088

7 January 2021

10.1371/JOURNAL.PBIO.0040088

Identifiers

DOI

1 reference

1 reference

1 reference

16683862

1 reference