Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example (Q44611790)

4 December 2017

Quantification and relative severity of inflated branch-support values generated by alternative methods: an empirical example (English)

1 reference

4 December 2017

Mark P Simmons

1

1 reference

PubMed ID

23403225

4 December 2017

Andrew P Norton

series ordinal

2

1 reference

4 December 2017

9 February 2013

1 reference

Molecular Phylogenetics and Evolution

4 December 2017

1 reference

4 December 2017

67

1 reference

4 December 2017

1

1 reference

4 December 2017

277-296

1 reference

A new view of insect-crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics.

4 December 2017

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Morphological phylogeny of the variable fly family Stratiomyidae (Insecta, Diptera)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Homoplasy and clade support

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Phylogeny and classification of the subfamily Rubioideae (Rubiaceae)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Comparing bootstrap and posterior probability values in the four-taxon case

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Gene Trees and Species Trees: Molecular Systematics as One-Character Taxonomy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

The Irrelevance of Allele Tree Topologies for Species Delimitation, and a Non-Topological Alternative

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Bootstrap confidence levels for phylogenetic trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

The devil in the details: interactions between the branch-length prior and likelihood model affect node support and branch lengths in the phylogeny of the Psoraceae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Confidence Limits on Phylogenies: an Approach using the Bootstrap

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Multiple quaternary refugia in the eastern Guiana shield revealed by comparative phylogeography of 12 frog species

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Linked branch support and tree stability

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Resolution of a supertree/supermatrix paradox

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

TNT, a free program for phylogenetic analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Is it better to add taxa or characters to a difficult phylogenetic problem?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Phylogeny of the Herbaceous Tribe Spermacoceae (Rubiaceae) Based on Plastid DNA Data1

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Phylogeny of the Asian Hedyotis-Oldenlandia complex (Spermacoceae, Rubiaceae): evidence for high levels of polyphyly and the parallel evolution of diplophragmous capsules

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Inferring complex phylogenies.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Taxonomic sampling, phylogenetic accuracy, and investigator bias

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

An Empirical Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Phylogeny estimation: traditional and Bayesian approaches

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Supermatrices, supertrees and serendipitous scaffolding: inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

A Concern for Evidence and a Phylogenetic Hypothesis of Relationships Among Epicrates (Boidae, Serpentes)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Outgroup Analysis and Parsimony

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

The misleading effects of composite taxa in supermatrices

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Delimitation of the Segregate Genera of Maytenus s. l. (Celastraceae) Based on Morphological and Molecular Characters

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Increasing the efficiency of searches for the maximum likelihood tree in a phylogenetic analysis of up to 150 nucleotide sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Strange bayes indeed: uniform topological priors imply non-uniform clade priors

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

jModelTest: phylogenetic model averaging

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Analyzing large data sets: rbcL 500 revisited

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

MrBayes 3: Bayesian phylogenetic inference under mixed models

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Parametric phylogenetics?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Phylogenomics with incomplete taxon coverage: the limits to inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Spurious 99% bootstrap and jackknife support for unsupported clades.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Phylogeny of Celastraceae Subfamilies Cassinoideae and Tripterygioideae Inferred from Morphological Characters and Nuclear and Plastid Loci

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Phylogeny of Celastraceae tribe Euonymeae inferred from morphological characters and nuclear and plastid genes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

How Meaningful Are Bayesian Support Values?

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

A 567‐Taxon Data Set for Angiosperms: The Challenges Posed by Bayesian Analyses of Large Data Sets

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Maximum Likelihood Analyses of 3,490 rbcL Sequences: Scalability of Comprehensive Inference versus Group-Specific Taxon Sampling

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

A rapid bootstrap algorithm for the RAxML Web servers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

Relaxed molecular clocks, the bias-variance trade-off, and the quality of phylogenetic inference

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Missing data and the design of phylogenetic analyses

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes)

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

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.2013.01.020

Phylogeny and Delimitation of the Celastrales Inferred from Nuclear and Plastid Genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMPEV.2013.01.020

10.1016/J.YMPEV.2013.01.020

7 January 2021

Identifiers

DOI

1 reference

4 December 2017

1 reference

PubMed ID

23403225