(Q40391766)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

title

ImOSM: intermittent evolution and robustness of phylogenetic methods (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

author name string

Minh Anh Thi Nguyen

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

Arndt von Haeseler

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

language of work or name

1 reference

22 September 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

Molecular Biology and Evolution

13 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

volume

29

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

issue

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

page(s)

663-673

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree

13 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Long-branch attraction bias and inconsistency in Bayesian phylogenetics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

INDELible: a flexible simulator of biological sequence evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

A rapid bootstrap algorithm for the RAxML Web servers

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

A mixed branch length model of heterotachy improves phylogenetic accuracy

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Bayesian estimation of sequence damage in ancient DNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Heterotachy and long-branch attraction in phylogenetics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Tracing the decay of the historical signal in biological sequence data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Testing substitution models within a phylogenetic tree

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Heterotachy, an important process of protein evolution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

MRBAYES: Bayesian inference of phylogenetic trees

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

MODELTEST: testing the model of DNA substitution

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Estimation of evolutionary distances between homologous nucleotide sequences

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

The impact of single substitutions on multiple sequence alignments

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

MISFITS: evaluating the goodness of fit between a phylogenetic model and an alignment.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

General heterotachy and distance method adjustments.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Accommodating the effect of ancient DNA damage on inferences of demographic histories

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Bayesian inference of errors in ancient DNA caused by postmortem degradation.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

In silico sequence evolution with site-specific interactions along phylogenetic trees.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Heterotachy and tree building: a case study with plastids and eubacteria.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

pIQPNNI: parallel reconstruction of large maximum likelihood phylogenies.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

The importance of proper model assumption in bayesian phylogenetics.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

IQPNNI: moving fast through tree space and stopping in time.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

On the conservation of protein sequences in evolution

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Topological bias and inconsistency of maximum likelihood using wrong models.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Statistical tests of models of DNA substitution.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates Are Heterotachous

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258038

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?

2 December 2018

1 reference

12 December 2020

Robustness of maximum likelihood tree estimation against different patterns of base substitutions

1 reference

12 December 2020

On the maximum likelihood method in molecular phylogenetics

1 reference

12 December 2020

How often do wrong models produce better phylogenies?

1 reference

12 December 2020

Likelihood, parsimony, and heterogeneous evolution

1 reference

12 December 2020

A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous

1 reference

12 December 2020

Identifiers

DOI

10.1093/MOLBEV/MSR220

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21940641%20AND%20SRC:MED&resulttype=core&format=json

13 February 2020

PubMed publication ID

21940641

1 reference