Resolving difficult phylogenetic questions: why more sequences are not enough (Q21092718)

15 August 2022

Hervé Philippe

Hervé

Philippe

1 reference

15 August 2022

Dennis V Lavrov

Dennis V

Lavrov

1 reference

15 August 2022

Gert Wörheide

Gert

Wörheide

1 reference

21423652

15 August 2022

D. Timothy J. Littlewood

series ordinal

object named as

D Timothy J Littlewood

author given names

D Timothy J

author last names

Littlewood

1 reference

15 August 2022

Denis Baurain

Denis

Baurain

1 reference

15 August 2022

Michael Manuel

Michael

Manuel

1 reference

21423652

Creative Commons Attribution 4.0 International

15 August 2022

language of work or name

English

0 references

publication date

March 2011

0 references

0 references

0 references

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e1000602

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start time

15 March 2011

1 reference

April 2022 Public Data File from Crossref

copyrighted

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cites work

Assessing the root of bilaterian animals with scalable phylogenomic methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Fast statistical alignment

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Concatenated analysis sheds light on early metazoan evolution and fuels a modern "urmetazoon" hypothesis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Recent evolutions of multiple sequence alignment algorithms

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Mitochondrial genome of Trichoplax adhaerens supports placozoa as the basal lower metazoan phylum

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Bayesian coestimation of phylogeny and sequence alignment

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

The COG database: new developments in phylogenetic classification of proteins from complete genomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Broad phylogenomic sampling improves resolution of the animal tree of life

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

A general empirical model of protein evolution derived from multiple protein families using 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=3057953

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

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=3057953

Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Phylogenomics revives traditional views on deep animal relationships

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Phylogenomics: the beginning of incongruence?

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Phylogenomics and the reconstruction of the tree of life

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Increased taxon sampling greatly reduces phylogenetic error

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Rooting the eutherian tree: the power and pitfalls of phylogenomics

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

RAxML-III: a fast program for maximum likelihood-based inference of large 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=3057953

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement 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=3057953

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=3057953

Gene tree discordance, phylogenetic inference and the multispecies coalescent

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

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=3057953

A new method for calculating evolutionary substitution rates

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Homology a personal view on some of the problems

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Joint Bayesian Estimation of Alignment and Phylogeny

10 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

28 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

A phylogenomic approach to resolve the arthropod tree of life

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Clytia hemisphaerica: a jellyfish cousin joins the laboratory.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Rapid likelihood analysis on large phylogenies using partial sampling of substitution histories

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Species tree inference by minimizing deep coalescences

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

The quest for orthologs: finding the corresponding gene across genomes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Estimating species trees using multiple-allele DNA 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=3057953

Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

A mixed branch length model of heterotachy improves phylogenetic accuracy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

A site- and time-heterogeneous model of amino acid replacement.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

A model of horizontal gene transfer and the bacterial phylogeny problem

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Protein evolution with dependence among codons due to tertiary structure.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Missing data, incomplete taxa, and phylogenetic accuracy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Maximum-Likelihood Models for Combined Analyses of Multiple 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=3057953

On the use of nucleic acid sequences to infer early branchings in the tree of life

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Inferring phylogenies from DNA sequences of unequal base compositions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Assessing site-interdependent phylogenetic models of sequence 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=3057953

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

Glass sponges and bilaterian animals share derived mitochondrial genomic features: a common ancestry or parallel evolution?

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

The number of nucleotides required to determine the branching order of three species, with special reference to the human-chimpanzee-gorilla divergence.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3057953

30 May 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

The closest BLAST hit is often not the nearest neighbor

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

Early evolution of the Metazoa and phylogenetic status of diploblasts as inferred from amino acid sequence of elongation factor-1 alpha

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

Conflicting phylogenetic signals at the base of the metazoan tree

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of Eumetazoa.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

Eubacterial phylogeny based on translational apparatus proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

Can Incomplete Taxa Rescue Phylogenetic Analyses from Long-Branch Attraction?

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

Conjugate Gibbs sampling for Bayesian phylogenetic models

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

Detecting and Overcoming Systematic Errors in Genome-Scale Phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PBIO.1000602

How good are deep phylogenetic trees?

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/21423652

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Taxonomic sampling, phylogenetic accuracy, and investigator bias

1 reference

https://pubmed.ncbi.nlm.nih.gov/21423652

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PBIO.1000602

1 reference

release_qth4lq6qwvflda4jewizcwiykm

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/qth4lq6qwvflda4jewizcwiykm

mapped directly with Wikidata item

24 November 2022

based on heuristic

1 reference

1 reference

21423652

1 reference