Heterotachy and long-branch attraction in phylogenetics (Q21283964)

19 August 2022

5

Frédéric Delsuc

Frédéric

Delsuc

1 reference

19 August 2022

1

Hervé Philippe

Hervé

Philippe

1 reference

19 August 2022

Yan Zhou

2

Yan

Zhou

1 reference

1037474535

19 August 2022

Nicolas Rodrigue

series ordinal

4

author given names

Nicolas

author last names

Rodrigue

1 reference

1037474535

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

19 August 2022

language of work or name

English

0 references

publication date

2005

0 references

published in

BMC Evolutionary Biology

0 references

volume

5

0 references

issue

1

0 references

page(s)

50

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=1274308

Heterotachy, an important process of protein evolution

19 March 2017

1 reference

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An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

''R"--project for statistical computing

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and Protostomia

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic 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=1274308

The nonidentity of invariable positions in the cytochromes c of different species

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Should phylogenetic models be trying to "fit an elephant"?

10 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Tracing the decay of the historical signal in biological sequence 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=1274308

A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state 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=1274308

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Phylogeny estimation: traditional and Bayesian approaches

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Evolution of chlorophyll and bacteriochlorophyll: the problem of invariant sites in sequence analysis

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Success of maximum likelihood phylogeny inference in the four-taxon case

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Substitutional bias confounds inference of cyanelle origins from sequence 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=1274308

Fitting Discrete Probability Distributions to Evolutionary Events

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

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

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Monophyly of primary photosynthetic eukaryotes: green plants, red algae, and glaucophytes

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Maximum Likelihood Outperforms Maximum Parsimony Even When Evolutionary Rates Are Heterotachous

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

No magic pill for phylogenetic error

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Covarion structure in plastid genome evolution: a new statistical test

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies.

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Is the Felsenstein zone a fly trap?

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Archaeal phylogeny based on ribosomal proteins

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

Eubacterial phylogeny based on translational apparatus proteins

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

On the conservation of protein sequences in 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=1274308

Opinion: long branch attraction and protist 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=1274308

Phylogeny of eukaryotes based on ribosomal RNA: long-branch attraction and models of 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=1274308

The root of the tree of life in the light of the covarion model

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1274308

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?

29 November 2018

1 reference

12 December 2020

How molecules evolve in eubacteria

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

10.1186/1471-2148-5-50

1 reference

https://scigraph.springernature.com/pub.10.1186/1471-2148-5-50

1 reference

9 September 2019

1 reference

1 reference

PubMed publication ID

16209710

1 reference