Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization
Published 2019 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Ultraconserved element (UCE) probe set design: Base genome and initial design parameters critical for optimization
Authors
Keywords
-
Journal
Ecology and Evolution
Volume -, Issue -, Pages -
Publisher
Wiley
Online
2019-06-12
DOI
10.1002/ece3.5260
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Phylogenomics and species delimitation of a complex radiation of Neotropical suboscine birds ( Pachyramphus )
- (2018) Lukas J. Musher et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Evaluating methods for phylogenomic analyses, and a new phylogeny for a major frog clade (Hyloidea) based on 2214 loci
- (2018) Jeffrey W. Streicher et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Evolutionary history of Coleoptera revealed by extensive sampling of genes and species
- (2018) Shao-Qian Zhang et al. Nature Communications
- Quantifying the unquantifiable: why Hymenoptera, not Coleoptera, is the most speciose animal order
- (2018) Andrew A. Forbes et al. BMC ECOLOGY
- Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements
- (2017) Jacob A. Esselstyn et al. Genome Biology and Evolution
- Genome-wide survey of nuclear protein-coding markers for beetle phylogenetics and their application in resolving both deep and shallow-level divergences
- (2017) Li-Heng Che et al. Molecular Ecology Resources
- BaitsTools: Software for hybridization capture bait design
- (2017) Michael G. Campana Molecular Ecology Resources
- Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems
- (2017) Andrea M. Quattrini et al. Molecular Ecology Resources
- Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens
- (2017) Sara Ruane et al. Molecular Ecology Resources
- Sequencing historical specimens: successful preparation of small specimens with low amounts of degraded DNA
- (2017) John S. Sproul et al. Molecular Ecology Resources
- How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes)
- (2017) Peter A. Hosner et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Systematics of aquatic beetles (Coleoptera): current state and future directions
- (2017) ANDREW EDWARD Z. SHORT SYSTEMATIC ENTOMOLOGY
- Ultraconserved elements show utility in phylogenetic inference of Adephaga (Coleoptera) and suggest paraphyly of ‘Hydradephaga’
- (2017) STEPHEN M. BACA et al. SYSTEMATIC ENTOMOLOGY
- Tip-dated phylogeny of whirligig beetles reveals ancient lineage surviving on Madagascar
- (2017) Grey T. Gustafson et al. Scientific Reports
- Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils
- (2017) Matthew H. Van Dam et al. PLoS One
- Optimization of signal-to-noise ratio for efficient microarray probe design
- (2016) Olga V. Matveeva et al. BIOINFORMATICS
- The Eurasian invasion: phylogenomic data reveal multiple Southeast Asian origins for Indian Dragon Lizards
- (2016) Jesse L. Grismer et al. BMC EVOLUTIONARY BIOLOGY
- Genomic data reveals potential for hybridization, introgression, and incomplete lineage sorting to confound phylogenetic relationships in an adaptive radiation of narrow-mouth frogs
- (2016) Alana M. Alexander et al. EVOLUTION
- BaitFisher: A Software Package for Multispecies Target DNA Enrichment Probe Design
- (2016) Christoph Mayer et al. MOLECULAR BIOLOGY AND EVOLUTION
- Capturing Darwin's dream
- (2016) Travis C. Glenn et al. Molecular Ecology Resources
- High phylogenetic utility of an ultraconserved element probe set designed for Arachnida
- (2016) James Starrett et al. Molecular Ecology Resources
- Experimental conditions improving in-solution target enrichment for ancient DNA
- (2016) Diana I. Cruz-Dávalos et al. Molecular Ecology Resources
- Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus:Piranga)
- (2016) Joseph D. Manthey et al. SYSTEMATIC BIOLOGY
- The peril of dating beetles
- (2016) EMMANUEL F. A. TOUSSAINT et al. SYSTEMATIC ENTOMOLOGY
- HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment
- (2016) Matthew G. Johnson et al. Applications in Plant Sciences
- Sequence Capture and Phylogenetic Utility of Genomic Ultraconserved Elements Obtained from Pinned Insect Specimens
- (2016) Bonnie B. Blaimer et al. PLoS One
- BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
- (2015) Felipe A. Simão et al. BIOINFORMATICS
- PHYLUCE is a software package for the analysis of conserved genomic loci
- (2015) Brant C. Faircloth BIOINFORMATICS
- Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants
- (2015) Bonnie B. Blaimer et al. BMC EVOLUTIONARY BIOLOGY
- Impact of enrichment conditions on cross-species capture of fresh and degraded DNA
- (2015) Johanna L. A. Paijmans et al. Molecular Ecology Resources
- Sequence capture of ultraconserved elements from bird museum specimens
- (2015) John E. McCormack et al. Molecular Ecology Resources
- The beetle tree of life reveals that Coleoptera survived end-Permian mass extinction to diversify during the Cretaceous terrestrial revolution
- (2015) DUANE D. MCKENNA et al. SYSTEMATIC ENTOMOLOGY
- Successful Recovery of Nuclear Protein-Coding Genes from Small Insects in Museums Using Illumina Sequencing
- (2015) Kojun Kanda et al. PLoS One
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
- (2014) Lam-Tung Nguyen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera
- (2014) Brant C. Faircloth et al. Molecular Ecology Resources
- The evolution of peafowl and other taxa with ocelli (eyespots): a phylogenomic approach
- (2014) K. Sun et al. PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
- (2013) John E. McCormack et al. PLoS One
- A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)
- (2013) Brant C. Faircloth et al. PLoS One
- Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales
- (2013) Brian Tilston Smith et al. SYSTEMATIC BIOLOGY
- More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs
- (2012) N. G. Crawford et al. Biology Letters
- Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries
- (2012) Jesse Dabney et al. BIOTECHNIQUES
- Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)
- (2012) Ylenia Chiari et al. BMC BIOLOGY
- Phylogeny of Bembidion and related ground beetles (Coleoptera: Carabidae: Trechinae: Bembidiini: Bembidiina)
- (2012) David R. Maddison MOLECULAR PHYLOGENETICS AND EVOLUTION
- Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
- (2012) Brant C. Faircloth 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
- Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles
- (2011) X.-X. Shen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Applications of next-generation sequencing to phylogeography and phylogenetics
- (2011) John E. McCormack et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Fast and accurate long-read alignment with Burrows–Wheeler transform
- (2010) Heng Li et al. BIOINFORMATICS
- Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads
- (2010) G. Lunter et al. GENOME RESEARCH
- The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- (2010) A. McKenna et al. GENOME RESEARCH
- Target-enrichment strategies for next-generation sequencing
- (2010) Lira Mamanova et al. NATURE METHODS
- A preliminary characterization of Bembidion perspicuum LeConte, with a reclassification of related species (Coleoptera, Carabidae) north of México
- (2010) David Maddison et al. ZooKeys
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Enrichment of sequencing targets from the human genome by solution hybridization
- (2009) Ryan Tewhey et al. GENOME BIOLOGY
- Monophyly of terrestrial adephagan beetles as indicated by three nuclear genes (Coleoptera: Carabidae and Trachypachidae)
- (2008) David R. Maddison et al. ZOOLOGICA SCRIPTA
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started