Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

Phylogenomics of Horned Lizards (Genus:Phrynosoma) Using Targeted Sequence Capture Data

(2015) Adam D. Leaché et al.   COPEIA

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

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears

(2014) Shiping Liu et al.   CELL

Use of RAD sequencing for delimiting species

(2014) E Pante et al.   HEREDITY

A New Species of Horned Lizard (GenusPhrynosoma) from Guerrero, México, with an Updated Multilocus Phylogeny

(2014) Adrián Nieto-Montes de Oca et al.   HERPETOLOGICA

Empirical Assessment of RAD Sequencing for Interspecific Phylogeny

(2014) Astrid Cruaud et al.   MOLECULAR BIOLOGY AND EVOLUTION

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Automated Reconstruction of Whole-Genome Phylogenies from Short-Sequence Reads

(2014) Frederic Bertels et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diversification and asymmetrical gene flow across time and space: lineage sorting and hybridization in polytypic barking frogs

(2014) Jeffrey W. Streicher et al.   MOLECULAR ECOLOGY

Demystifying the RAD fad

(2014) Jonathan B. Puritz et al.   MOLECULAR ECOLOGY

The advantages of going large: genome-wide SNPs clarify the complex population history and systematics of the threatened western pond turtle

(2014) Phillip Q. Spinks et al.   MOLECULAR ECOLOGY

Restriction site-associated DNA sequencing, genotyping error estimation andde novoassembly optimization for population genetic inference

(2014) A. Mastretta-Yanes et al.   Molecular Ecology Resources

Dubious resolution and support from published sparse supermatrices: The importance of thorough tree searches

(2014) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2014) Huateng Huang et al.   SYSTEMATIC BIOLOGY

DIVERSITY AND NICHE EVOLUTION ALONG ARIDITY GRADIENTS IN NORTH AMERICAN LIZARDS (PHRYNOSOMATIDAE)

(2013) John J. Wiens et al.   EVOLUTION

Correcting Coalescent Analyses for Panel-Based SNP Ascertainment

(2013) J. R. McGill et al.   GENETICS

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Phylogenetic Signal Variation in the Genomes of Medicago (Fabaceae)

(2013) Jeremy B. Yoder et al.   SYSTEMATIC BIOLOGY

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

Special features of RAD Sequencing data: implications for genotyping

(2012) John W. Davey et al.   MOLECULAR ECOLOGY

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

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

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

THE IMPACT OF GENE-TREE/SPECIES-TREE DISCORDANCE ON DIVERSIFICATION-RATE ESTIMATION

(2011) Frank T. Burbrink et al.   EVOLUTION

Statistics and Truth in Phylogenomics

(2011) S. Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms

(2011) J. E. SEEB et al.   Molecular Ecology Resources

Quartet MaxCut: A fast algorithm for amalgamating quartet trees

(2011) Sagi Snir et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Resolving postglacial phylogeography using high-throughput sequencing

(2010) K. J. Emerson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data, and a revised phylogeny for Sceloporus

(2009) John J. Wiens et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Homoplasy and Clade Support

(2009) Matthew C. Brandley et al.   SYSTEMATIC BIOLOGY

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One