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

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

More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

(2012) N. G. Crawford et al.   Biology Letters

Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence

(2012) MD. Shamsuzzoha Bayzid et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A Phylogenetic Perspective on the Evolution of Mediterranean Teleost Fishes

(2012) Christine N. Meynard et al.   PLoS One

Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels

(2012) Brant C. Faircloth et al.   PLoS One

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Evolution of Pharyngognathy: A Phylogenetic and Functional Appraisal of the Pharyngeal Jaw Key Innovation in Labroid Fishes and Beyond

(2012) P. C. Wainwright et al.   SYSTEMATIC BIOLOGY

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

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

(2009) Francesco Santini et al.   BMC EVOLUTIONARY BIOLOGY

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Enrichment of sequencing targets from the human genome by solution hybridization

(2009) Ryan Tewhey et al.   GENOME BIOLOGY

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

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

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

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

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

(2008) A. Stamatakis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Optimal Data Partitioning and a Test Case for Ray-Finned Fishes (Actinopterygii) Based on Ten Nuclear Loci

(2008) Chenhong Li et al.   SYSTEMATIC BIOLOGY