Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data (Q34069982)

30 July 2017

Radical instability and spurious branch support by likelihood when applied to matrices with non-random distributions of missing data (English)

1 reference

30 July 2017

1 reference

Mark P Simmons

1

1 reference

30 July 2017

31 October 2011

1 reference

Molecular Phylogenetics and Evolution

30 July 2017

1 reference

30 July 2017

62

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30 July 2017

1

1 reference

30 July 2017

472-484

1 reference

A new look at the statistical model identification

30 July 2017

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

A Dated Phylogeny of Marsupials Using a Molecular Supermatrix and Multiple Fossil Constraints

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

The use and validity of composite taxa in phylogenetic analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Inconsistency of evolutionary tree topology reconstruction methods when substitution rates vary across characters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Molecular phylogenetics, temporal diversification, and principles of evolution in the mustard family (Brassicaceae).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Phylogenomic Analysis of BAC-end Sequence Libraries in Oryza (Poaceae)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Data decisiveness, data quality, and incongruence in phylogenetic analysis: an example from the monocotyledons using mitochondrial atp A sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Molecular phylogenetics of myliobatiform fishes (Chondrichthyes: Myliobatiformes), with comments on the effects of missing data on parsimony and likelihood.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Bootstrap confidence levels for phylogenetic trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Maximum Likelihood and Minimum-Steps Methods for Estimating Evolutionary Trees from Data on Discrete Characters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Confidence Limits on Phylogenies: an Approach using the Bootstrap

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Molecular phylogeny of the carnivora (mammalia): assessing the impact of increased sampling on resolving enigmatic relationships

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple gene data sets

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Linked branch support and tree stability

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Resolution of a supertree/supermatrix paradox

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

MaxAlign: maximizing usable data in an alignment

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Phylogeny and divergence of the pinnipeds (Carnivora: Mammalia) assessed using a multigene dataset.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Parametric models for incomplete continuous and categorical longitudinal data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

The misleading effects of composite taxa in supermatrices

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

The efficiency of different search strategies in estimating parsimony jackknife, bootstrap, and Bremer support

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

jModelTest: phylogenetic model averaging

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

A likelihood look at the supermatrix-supertree controversy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

MrBayes 3: Bayesian phylogenetic inference under mixed models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Improved bootstrap confidence limits in large-scale phylogenies, with an example from Neo-Astragalus (Leguminosae).

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Phylogenomics with incomplete taxon coverage: the limits to inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Misleading results of likelihood-based phylogenetic analyses in the presence of missing data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Spurious 99% bootstrap and jackknife support for unsupported clades.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Alignment of, and phylogenetic inference from, random sequences: the susceptibility of alternative alignment methods to creating artifactual resolution and support.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

A simulation study comparing supertree and combined analysis methods using SMIDGen

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

A supermatrix-based molecular phylogeny of the family Drosophilidae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Does adding characters with missing data increase or decrease phylogenetic accuracy?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Missing data, incomplete taxa, and phylogenetic accuracy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Missing data and the design of phylogenetic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

Missing data in phylogenetic analysis: reconciling results from simulations and empirical data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2011.10.017

10.1016/J.YMPEV.2011.10.017

7 January 2021

Identifiers

DOI

1 reference

30 July 2017

1 reference

PubMed ID

22067131