(Q46286546)

21 December 2017

title

To include or not to include: The Impact of Gene Filtering on Species Tree Estimation Methods (English)

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21 December 2017

2

Tandy Warnow

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21 December 2017

author name string

Erin K Molloy

series ordinal

1

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21 December 2017

publication date

15 September 2017

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21 December 2017

published in

Systematic Biology

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21 December 2017

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes

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21 January 2018

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Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

21 January 2018

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Quartet inference from SNP data under the coalescent model

21 January 2018

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Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

21 January 2018

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

21 January 2018

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A comparative study of SVDquartets and other coalescent-based species tree estimation methods

21 January 2018

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Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method

21 January 2018

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Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

21 January 2018

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Phylogenomics and species delimitation in the knob-scaled lizards of the genus Xenosaurus (Squamata: Xenosauridae) using ddRADseq data reveal a substantial underestimation of diversity

21 January 2018

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Fast and consistent estimation of species trees using supermatrix rooted triples

21 January 2018

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Robustness to divergence time underestimation when inferring species trees from estimated gene trees

21 January 2018

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Gene tree discordance, phylogenetic inference and the multispecies coalescent

21 January 2018

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New insights on the sister lineage of percomorph fishes with an anchored hybrid enrichment dataset

21 January 2018

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Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

21 January 2018

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Prospects for building the tree of life from large sequence databases

21 January 2018

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Is a new and general theory of molecular systematics emerging?

21 January 2018

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High-resolution species trees without concatenation

21 January 2018

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Sequence length bounds for resolving a deep phylogenetic divergence.

21 January 2018

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INDELible: a flexible simulator of biological sequence evolution

21 January 2018

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

21 January 2018

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Bayesian inference of species trees from multilocus data

21 January 2018

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Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection

21 January 2018

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Avoiding Missing Data Biases in Phylogenomic Inference: An Empirical Study in the Landfowl (Aves: Galliformes).

21 January 2018

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Effects of missing data on species tree estimation under the coalescent

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods

21 January 2018

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Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences

21 January 2018

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MRBAYES: Bayesian inference of phylogenetic trees

21 January 2018

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

21 January 2018

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iGLASS: an improvement to the GLASS method for estimating species trees from gene trees.

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Should genes with missing data be excluded from phylogenetic analyses?

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

ExaML version 3: a tool for phylogenomic analyses on supercomputers

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

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

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Inconsistency of phylogenetic estimates from concatenated data under coalescence

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

How low can you go? The effects of mutation rate on the accuracy of species-tree estimation

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Applying species-tree analyses to deep phylogenetic histories: challenges and potential suggested from a survey of empirical phylogenetic studies

21 January 2018

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Phylogenomics of phrynosomatid lizards: conflicting signals from sequence capture versus restriction site associated DNA sequencing

21 January 2018

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Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

21 January 2018

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

21 January 2018

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Estimating phylogenetic trees from genome-scale data

21 January 2018

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Estimating species trees from unrooted gene trees.

21 January 2018

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Estimating species phylogenies using coalescence times among sequences.

21 January 2018

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Phylogenomic analysis of a rapid radiation of misfit fishes (Syngnathiformes) using ultraconserved elements

21 January 2018

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SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

21 January 2018

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Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

21 January 2018

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Maximum likelihood estimates of species trees: how accuracy of phylogenetic inference depends upon the divergence history and sampling design

21 January 2018

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Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods.

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Statistical binning enables an accurate coalescent-based estimation of the avian tree

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

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

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

ASTRAL: genome-scale coalescent-based species tree estimation

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

StarBEAST2 brings faster species tree inference and accurate estimates of substitution rates

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Phylogenomics for Systematic Biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Accurate phylogenetic tree reconstruction from quartets: a heuristic approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Recovering the treelike trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Inferring ancient divergences requires genes with strong phylogenetic signals.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Novel information theory-based measures for quantifying incongruence among phylogenetic trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

The effects of subsampling gene trees on coalescent methods applied to ancient divergences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Quartet MaxCut: a fast algorithm for amalgamating quartet trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Inconsistency of Species Tree Methods under Gene Flow.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

21 January 2018

The gene tree delusion

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

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%2FSYSBIO%2FSYX077

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%2FSYSBIO%2FSYX077

Phylogenomic analyses reveal novel relationships among snake families

21 January 2018

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https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

DendroPy: a Python library for phylogenetic computing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Bootstrap support is not first-order correct.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

The probability of correctly resolving a split as an experimental design criterion in phylogenetics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Cross-species gene transfer; implications for a new theory of evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Taxon sampling and the optimal rates of evolution for phylogenetic inference.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Phylogenetic signal and noise: predicting the power of a data set to resolve phylogeny

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

The Impact of Missing Data on Species Tree Estimation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

BBCA: Improving the scalability of *BEAST using random binning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

Bootstrapping Phylogenetic Trees: Theory and Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYX077

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYX077

1 reference

21 December 2017

1 reference

21 December 2017