The impact of modelling rate heterogeneity among sites on phylogenetic estimates of intraspecific evolutionary rates and timescales (Q28657958)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Nathan Lo

2

Nathan

Lo

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

Simon Y W Ho

series ordinal

3

author given names

Simon Y W

author last names

Ho

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

language of work or name

English

0 references

publication date

2014

0 references

published in

PLOS One

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

issue

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

page(s)

e95722

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

2 June 2020

copyright license

start time

5 May 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

maintained by WikiProject

1 reference

Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

A revised timescale for human evolution based on ancient mitochondrial genomes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Bayesian phylogenetics with BEAUti and the BEAST 1.7

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

FastTree 2--approximately maximum-likelihood trees for large alignments

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Correcting for purifying selection: an improved human mitochondrial molecular clock

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Relaxed phylogenetics and dating with confidence

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

SIMMAP: stochastic character mapping of discrete traits on phylogenies

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Late Quaternary loss of genetic diversity in muskox (Ovibos).

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

MUSCLE: multiple sequence alignment with high accuracy and high throughput

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Mitochondrial genome variation and the origin of modern humans

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

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

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

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=4010409

Among-site rate variation and its impact on phylogenetic analyses

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Bayesian selection of continuous-time Markov chain evolutionary models

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

A method for estimating the number of invariant amino acid coding positions in a gene using cytochrome c as a model case

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

An estimation of the number of invariable sites is necessary for the accurate estimation of the number of nucleotide substitutions since a common ancestor

9 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated

9 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Arrival of Paleo-Indians to the southern cone of South America: new clues from mitogenomes

9 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Bayesian selection of nucleotide substitution models and their site assignments

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Variation in the mutation rate across mammalian genomes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Performance of criteria for selecting evolutionary models in phylogenetics: a comprehensive study based on simulated datasets

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Hantavirus evolution in relation to its rodent and insectivore hosts: no evidence for codivergence

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Direct estimation of per nucleotide and genomic deleterious mutation rates in Drosophila

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

An empirical examination of the utility of codon-substitution models in phylogeny reconstruction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Taking variation of evolutionary rates between sites into account in inferring phylogenies

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Large differences in substitutional pattern and evolutionary rate of 12S ribosomal RNA genes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Rates of molecular evolution and the fraction of nucleotide positions free to vary

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Incorporating Molecular Evolution into Phylogenetic Analysis, and a New Compilation of Conserved Polymerase Chain Reaction Primers for Animal Mitochondrial DNA

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095722

Substitution rate variation among sites in hypervariable region 1 of human mitochondrial DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095722

The influence of rate heterogeneity among sites on the time dependence of molecular rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095722

A gamma mixture model better accounts for among site rate heterogeneity

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095722

Evolutionary distances between nucleotide sequences based on the distribution of substitution rates among sites as estimated by parsimony.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095722

Estimating the Dimension of a Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095722

Bayesian estimation of substitution rates from ancient DNA sequences with low information content

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095722

Mutation Load: The Fitness of Individuals in Populations Where Deleterious Alleles Are Abundant

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0095722

Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4010409

Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites

27 November 2018

1 reference

12 December 2020

Mapping mutations on phylogenies

1 reference

12 December 2020

General time-reversible distances with unequal rates across sites: mixing gamma and inverse Gaussian distributions with invariant sites

1 reference

12 December 2020

Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated?

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0095722

Identifiers

DOI

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json

2 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24798481%20AND%20SRC:MED&resulttype=core&format=json