(Q31026927)

28 June 2017

title

The Impact of Missing Data on Species Tree Estimation (English)

1 reference

28 June 2017

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Charles Cavender Davis

series ordinal

3

object named as

Charles C Davis

1 reference

28 June 2017

Zhenxiang Xi

1

1 reference

28 June 2017

Liang Liu

series ordinal

2

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28 June 2017

publication date

20 November 2015

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Molecular Biology and Evolution

28 June 2017

published in

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28 June 2017

volume

33

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28 June 2017

issue

3

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28 June 2017

page(s)

838-860

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The phylogeny of Cetartiodactyla: the importance of dense taxon sampling, missing data, and the remarkable promise of cytochrome b to provide reliable species-level phylogenies

28 June 2017

cites work

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Combining Trees as a Way of Combining Data Sets for Phylogenetic Inference, and the Desirability of Combining Gene Trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Integrating phylogenetic and population genetic analyses of multiple loci to test species divergence hypotheses in Passerina buntings

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Can deliberately incomplete gene sample augmentation improve a phylogeny estimate for the advanced moths and butterflies (Hexapoda: Lepidoptera)?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Explosive radiation of Malpighiales supports a mid-cretaceous origin of modern tropical rain forests

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

The supermatrix approach to systematics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Discordance of species trees with their most likely gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Gene tree discordance, phylogenetic inference and the multispecies coalescent

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Prospects for building the tree of life from large sequence databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Broad phylogenomic sampling improves resolution of the animal tree of life

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

MUSCLE: multiple sequence alignment with high accuracy and high throughput

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenetic analyses reveal the shady history of C4 grasses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Is a new and general theory of molecular systematics emerging?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

The evolutionary root of flowering plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Removal of noisy characters from chloroplast genome-scale data suggests revision of phylogenetic placements of Amborella and Ceratophyllum

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Assessing the root of bilaterian animals with scalable phylogenomic methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Bayesian inference of species trees from multilocus data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Effects of missing data on species tree estimation under the coalescent

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Whole-genome analyses resolve early branches in the tree of life of modern birds

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Should genes with missing data be excluded from phylogenetic analyses?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

A genome triplication associated with early diversification of the core eudicots

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

STEM: species tree estimation using maximum likelihood for gene trees under coalescence.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

The accuracy of species tree estimation under simulation: a comparison of methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

BEST: Bayesian estimation of species trees under the coalescent model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Coalescent methods are robust to the simultaneous effects of long branches and incomplete lineage sorting

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Estimating phylogenetic trees from genome-scale data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Estimating species trees from unrooted gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phybase: an R package for species tree analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Coalescent methods for estimating phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Estimating species phylogenies using coalescence times among sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Next-generation sequencing platforms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenetic supermatrix analysis of GenBank sequences from 2228 papilionoid legumes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

ASTRAL: genome-scale coalescent-based species tree estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Possible loss of the chloroplast genome in the parasitic flowering plant Rafflesia lagascae (Rafflesiaceae)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenomics of eukaryotes: impact of missing data on large alignments

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenetic inference based on matrix representation of trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Impact of missing data on phylogenies inferred from empirical phylogenomic data sets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Genome reduction in prokaryotic obligatory intracellular parasites of humans: a comparative analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Inferring ancient divergences requires genes with strong phylogenetic signals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenomics with incomplete taxon coverage: the limits to inference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Terraces in phylogenetic tree space

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Calculating bootstrap probabilities of phylogeny using multilocus sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

A confounding effect of missing data on character conflict in maximum likelihood and Bayesian MCMC phylogenetic analyses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Understanding angiosperm diversification using small and large phylogenetic trees

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Land plant origins and coalescence confusion

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

How Should Genes and Taxa be Sampled for Phylogenomic Analyses with Missing Data? An Empirical Study in Iguanian Lizards

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Sparse supermatrices for phylogenetic inference: taxonomy, alignment, rogue taxa, and the phylogeny of living turtles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Developing markers for multilocus phylogenetics in non-model organisms: A test case with turtles

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated Conditions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenomic analyses elucidate the evolutionary relationships of bats

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Methods for genomic partitioning

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Measuring the fit of sequence data to phylogenetic model: allowing for missing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Ancient rapid radiations of insects: challenges for phylogenetic analysis

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylotranscriptomic analysis of the origin and early diversification of land plants

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Missing data, incomplete taxa, and phylogenetic accuracy

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

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

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Coalescent versus concatenation methods and the placement of Amborella as sister to water lilies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenomics and coalescent analyses resolve extant seed plant relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Three keys to the radiation of angiosperms into freezing environments

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Systematic error in seed plant phylogenomics

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

Phylogenomic analysis resolves the interordinal relationships and rapid diversification of the laurasiatherian mammals

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1 reference

https://api.crossref.org/works/10.1093%2FMOLBEV%2FMSV266

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Identifiers

DOI

10.1093/MOLBEV/MSV266

1 reference

28 June 2017

1 reference