Evaluating the performance of anchored hybrid enrichment at the tips of the tree of life: a phylogenetic analysis of Australian Eugongylus group scincid lizards

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data

(2014) Ralph S Peters et al.   BMC EVOLUTIONARY BIOLOGY

Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing

(2014) Lisa N. Barrow et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Statistical binning enables an accurate coalescent-based estimation of the avian tree

(2014) S. Mirarab et al.   SCIENCE

Disentangling Methodological and Biological Sources of Gene Tree Discordance on Oryza (Poaceae) Chromosome 3

(2014) Derrick J. Zwickl et al.   SYSTEMATIC BIOLOGY

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Phylogenomics Resolves Evolutionary Relationships among Ants, Bees, and Wasps

(2013) Brian R. Johnson et al.   CURRENT BIOLOGY

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

De novotranscriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set

(2013) Sonal Singhal   Molecular Ecology Resources

Integrating phylogenetics, phylogeography and population genetics through genomes and evolutionary theory

(2013) Asher D. Cutter   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Transcriptome Sequences Resolve Deep Relationships of the Grape Family

(2013) Jun Wen et al.   PLoS One

Reproductive isolation between phylogeographic lineages scales with divergence

(2013) S. Singhal et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The evolution of viviparity: molecular and genomic data from squamate reptiles advance understanding of live birth in amniotes

(2013) James U Van Dyke et al.   REPRODUCTION

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

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

(2012) Ke Bi et al.   BMC GENOMICS

The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus)

(2012) Darin R Rokyta et al.   BMC GENOMICS

Uterine Gene Expression in the Live-Bearing Lizard, Chalcides ocellatus, Reveals Convergence of Squamate Reptile and Mammalian Pregnancy Mechanisms

(2012) Matthew C. Brandley et al.   Genome Biology and Evolution

Insect Phylogenomics: Exploring the Source of Incongruence Using New Transcriptomic Data

(2012) Sabrina Simon et al.   Genome Biology and Evolution

Concatenation and Concordance in the Reconstruction of Mouse Lemur Phylogeny: An Empirical Demonstration of the Effect of Allele Sampling in Phylogenetics

(2012) David W. Weisrock et al.   MOLECULAR BIOLOGY AND EVOLUTION

Maximum Likelihood Implementation of an Isolation-with-Migration Model with Three Species for Testing Speciation with Gene Flow

(2012) T. Zhu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parallel tagged amplicon sequencing reveals major lineages and phylogenetic structure in the North American tiger salamander (Ambystoma tigrinum) species complex

(2012) Eric M. O'Neill et al.   MOLECULAR ECOLOGY

Testing hypotheses for genealogical discordance in a rainforest lizard

(2012) Sonal Singhal et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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 Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC BIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Phylogeographic divergence in the widespread delicate skink (Lampropholis delicata) corresponds to dry habitat barriers in eastern Australia

(2011) David G Chapple et al.   BMC EVOLUTIONARY BIOLOGY

Lygosomine phylogeny and the origins of Australian scincid lizards

(2011) Adam Skinner et al.   JOURNAL OF BIOGEOGRAPHY

Biogeographic barriers in south-eastern Australia drive phylogeographic divergence in the garden skink, Lampropholis guichenoti

(2011) David G. Chapple et al.   JOURNAL OF BIOGEOGRAPHY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Directed next generation sequencing for phylogenetics: An example using Decapoda (Crustacea)

(2011) Seth M. Bybee et al.   ZOOLOGISCHER ANZEIGER

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

A Likelihood Ratio Test of Speciation with Gene Flow Using Genomic Sequence Data

(2010) Ziheng Yang   Genome Biology and Evolution

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

Variable responses of skinks to a common history of rainforest fluctuation: concordance between phylogeography and palaeo-distribution models

(2009) ADNAN MOUSSALLI et al.   MOLECULAR ECOLOGY

Origin, diversification, and systematics of the New Zealand skink fauna (Reptilia: Scincidae)

(2009) David G. Chapple et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data

(2009) Ryan N. Gutenkunst et al.   PLoS Genetics

Multilocus phylogeography and phylogenetics using sequence-based markers

(2008) Patrícia H. Brito et al.   GENETICA

Parallel evolution of placentation in Australian scincid lizards

(2008) James R. Stewart et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Placental ontogeny in Tasmanian snow skinks (genusNiveoscincus) (Lacertilia: Scincidae)

(2008) James R. Stewart et al.   JOURNAL OF MORPHOLOGY

Combined mitochondrial and nuclear data enhance resolution of a rapid radiation of Australian rainbow skinks (Scincidae: Carlia)

(2008) G DOLMAN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

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

Multilocus Phylogenetics of a Rapid Radiation in the Genus Thomomys (Rodentia: Geomyidae)

(2008) Natalia M. Belfiore et al.   SYSTEMATIC BIOLOGY