Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Misconceptions on Missing Data in RAD-seq Phylogenetics with a Deep-scale Example from Flowering Plants
Authors
Keywords
-
Journal
SYSTEMATIC BIOLOGY
Volume -, Issue -, Pages syw092
Publisher
Oxford University Press (OUP)
Online
2016-10-13
DOI
10.1093/sysbio/syw092
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- ddRAD-seq phylogenetics based on nucleotide, indel, and presence–absence polymorphisms: Analyses of two avian genera with contrasting histories
- (2016) Jeffrey M. DaCosta et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Estimating phylogenetic trees from genome-scale data
- (2015) Liang Liu et al. Annals of the New York Academy of Sciences
- Historical introgression among the American live oaks and the comparative nature of tests for introgression
- (2015) Deren A. R. Eaton et al. EVOLUTION
- Phylogenomics of Phrynosomatid Lizards: Conflicting Signals from Sequence Capture versus Restriction Site Associated DNA Sequencing
- (2015) Adam D. Leaché et al. Genome Biology and Evolution
- Evolutionary and biogeographical patterns of barnacles from deep-sea hydrothermal vents
- (2015) Santiago Herrera et al. MOLECULAR ECOLOGY
- A RAD-based phylogenetics for Orestias fishes from Lake Titicaca
- (2015) Tetsumi Takahashi et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased
- (2015) Zhenxiang Xi et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
- (2015) Richard O. Prum et al. NATURE
- Temperate radiations and dying embers of a tropical past: the diversification ofViburnum
- (2015) Elizabeth L. Spriggs et al. NEW PHYTOLOGIST
- Quantifying MCMC Exploration of Phylogenetic Tree Space
- (2015) Chris Whidden et al. SYSTEMATIC BIOLOGY
- Impacts of Terraces on Phylogenetic Inference
- (2015) Michael J. Sanderson et al. SYSTEMATIC BIOLOGY
- Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies
- (2015) Adam D. Leaché et al. SYSTEMATIC BIOLOGY
- Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
- (2015) Md Shamsuzzoha Bayzid et al. PLoS One
- A chloroplast tree for Viburnum (Adoxaceae) and its implications for phylogenetic classification and character evolution
- (2014) Wendy L. Clement et al. AMERICAN JOURNAL OF BOTANY
- Quartet Inference from SNP Data Under the Coalescent Model
- (2014) Julia Chifman et al. BIOINFORMATICS
- PyRAD: assembly of de novo RADseq loci for phylogenetic analyses
- (2014) Deren A. R. Eaton BIOINFORMATICS
- ASTRAL: genome-scale coalescent-based species tree estimation
- (2014) S. Mirarab et al. BIOINFORMATICS
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Phylogeny of Zebrafish, a “Model Species,” within Danio, a “Model Genus”
- (2014) Braedan M. McCluskey et al. MOLECULAR BIOLOGY AND EVOLUTION
- Application of RAD-based phylogenetics to complex relationships among variously related taxa in a species flock
- (2014) Tetsumi Takahashi et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: A case study in Carex (Cyperaceae)
- (2014) Marcial Escudero et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data
- (2014) Andrew L. Hipp et al. PLoS One
- Statistical binning enables an accurate coalescent-based estimation of the avian tree
- (2014) S. Mirarab et al. SCIENCE
- Whole-genome analyses resolve early branches in the tree of life of modern birds
- (2014) E. D. Jarvis et al. SCIENCE
- Weighted Quartets Phylogenetics
- (2014) Eliran Avni et al. SYSTEMATIC BIOLOGY
- Unforeseen Consequences of Excluding Missing Data from Next-Generation Sequences: Simulation Study of RAD Sequences
- (2014) Huateng Huang et al. SYSTEMATIC BIOLOGY
- Correcting for Sequencing Error in Maximum Likelihood Phylogeny Inference
- (2014) Mary K. Kuhner et al. G3-Genes Genomes Genetics
- Inferring ancient divergences requires genes with strong phylogenetic signals
- (2013) Leonidas Salichos et al. NATURE
- Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)
- (2013) Deren A. R. Eaton et al. SYSTEMATIC BIOLOGY
- Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization
- (2013) Marie Cariou et al. Ecology and Evolution
- EggLib: processing, analysis and simulation tools for population genetics and genomics
- (2012) Stéphane De Mita et al. BMC GENETICS
- Genome-wide patterns of divergence and gene flow across a butterfly radiation
- (2012) Nicola J. Nadeau et al. MOLECULAR ECOLOGY
- Population genomics based on low coverage sequencing: how low should we go?
- (2012) C. Alex Buerkle et al. MOLECULAR ECOLOGY
- Inferring Phylogenies from RAD Sequence Data
- (2012) Benjamin E. R. Rubin et al. PLoS One
- Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
- (2012) Brant K. Peterson et al. PLoS One
- Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
- (2012) Alan R. Lemmon et al. SYSTEMATIC BIOLOGY
- Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
- (2011) J. E. McCormack et al. GENOME RESEARCH
- Terraces in Phylogenetic Tree Space
- (2011) M. J. Sanderson et al. SCIENCE
- BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
- (2010) Bret R. Larget et al. BIOINFORMATICS
- Genome size differentiates co-occurring populations of the planktonic diatom Ditylum brightwellii (Bacillariophyta)
- (2010) Julie A Koester et al. BMC EVOLUTIONARY BIOLOGY
- Genotype Imputation
- (2009) Yun Li et al. Annual Review of Genomics and Human Genetics
- Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers
- (2008) Nathan A. Baird et al. PLoS One
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now