Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics (Q36049287)

11 August 2017

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title

Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics (English)

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11 August 2017

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4

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11 August 2017

3

Travis C Glenn

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11 August 2017

2

Brian Tilston Smith

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11 August 2017

Michael G Harvey

1

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PubMed ID

27288477

11 August 2017

Robb T Brumfield

series ordinal

5

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11 August 2017

10 June 2016

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11 August 2017

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11 August 2017

65

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11 August 2017

5

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11 August 2017

910-924

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Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

11 August 2017

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

RAD Capture (Rapture): Flexible and Efficient Sequence-Based Genotyping

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Trade-offs and utility of alternative RADseq methods: reply to Puritz et al.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Rapid SNP discovery and genetic mapping using sequenced RAD markers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Phylogeny and diversification of the largest avian radiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Ultraconserved Elements in the Human Genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Transcriptome-based exon capture enables highly cost-effective comparative genomic data collection at moderate evolutionary scales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Is RAD-seq suitable for phylogenetic inference? An in silico assessment and optimization

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Model selection as a tool for phylogeographic inference: an example from the willow Salix melanopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

A method for counting PCR template molecules with application to next-generation sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Stacks: an analysis tool set for population genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

De novo fragment assembly with short mate-paired reads: Does the read length matter?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

MulRF: a software package for phylogenetic analysis using multi-copy gene trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Amplification biases and consistent recovery of loci in a double-digest RAD-seq protocol

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Can We Identify Genes with Increased Phylogenetic Reliability?

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Errors in the polymerase chain reaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

DNA polymerase fidelity and the polymerase chain reaction

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Genome sequencing and population genomics in non-model organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

PHYLUCE is a software package for the analysis of conserved genomic loci

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

The effect of RAD allele dropout on the estimation of genetic variation within and between populations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Field guide to next-generation DNA sequencers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Impacts of degraded DNA on restriction enzyme associated DNA sequencing (RADSeq).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Next-generation museomics disentangles one of the largest primate radiations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

A tether for Woronin body inheritance is associated with evolutionary variation in organelle positioning

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Comparison of normalization methods for construction of large, multiplex amplicon pools for next-generation sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Genomic variation in a widespread Neotropical bird (Xenops minutus) reveals divergence, population expansion, and gene flow

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Targeted enrichment: maximizing orthologous gene comparisons across deep evolutionary time

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Genotype, haplotype and copy-number variation in worldwide human populations

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Human genome ultraconserved elements are ultraselected

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Evolution of Darwin's finches and their beaks revealed by genome sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

A hybrid phylogenetic-phylogenomic approach for species tree estimation in African Agama lizards with applications to biogeography, character evolution, and diversification

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Anchored hybrid enrichment for massively high-throughput phylogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Capturing protein-coding genes across highly divergent species

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Estimating species phylogenies using coalescence times among sequences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Target-enrichment strategies for next-generation sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga).

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Genotyping-by-sequencing in ecological and conservation genomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Molecular Inversion Probes for targeted resequencing in non-model organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Genotype and SNP calling from next-generation sequencing data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Bioinformatics challenges of new sequencing technology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Inferring phylogenies from RAD sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from a neutral model of DNA sequence polymorphism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Detection and removal of PCR duplicates in population genomic ddRAD studies by addition of a degenerate base region (DBR) in sequencing adapters

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

ABySS: a parallel assembler for short read sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Target capture and massively parallel sequencing of ultraconserved elements for comparative studies at shallow evolutionary time scales

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

RESTseq--efficient benchtop population genomics with RESTriction Fragment SEQuencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Comparison of solution-based exome capture methods for next generation sequencing

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Sequencing degraded DNA from non-destructively sampled museum specimens for RAD-tagging and low-coverage shotgun phylogenetics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Evidence of abundant purifying selection in humans for recently acquired regulatory functions

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

2b-RAD: a simple and flexible method for genome-wide genotyping

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

RNA-Seq: a revolutionary tool for transcriptomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

21 January 2018

The genome of a songbird

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Paired-end RAD-seq for de novo assembly and marker design without available reference

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Bayesian species delimitation using multilocus sequence data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Velvet: algorithms for de novo short read assembly using de Bruijn graphs

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Comparative genomic data of the Avian Phylogenomics Project

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

Adapterama IV: Sequence Capture of Dual-digest RADseq Libraries with Identifiable Duplicates (RADcap)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYW036

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYW036

1 reference

11 August 2017

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1 reference

PubMed ID

27288477