Phylogenomic analyses of species relationships in the genusSabal(Arecaceae) using targeted sequence capture

A preliminary evaluation of the ancestry of a putative Sabal hybrid (Arecaceae: Coryphoideae), and the description of a new nothospecies, Sabal × brazoriensis

(2016) DOUGLAS H. GOLDMAN et al.   Phytotaxa

BBCA: Improving the scalability of *BEAST using random binning

(2014) Théo Zimmermann et al.   BMC GENOMICS

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

A Target Enrichment Method for Gathering Phylogenetic Information from Hundreds of Loci: An Example from the Compositae

(2014) Jennifer R. Mandel et al.   Applications in Plant Sciences

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

Discordance of Species Trees with Their Most Likely Gene Trees: A Unifying Principle

(2013) N. A. Rosenberg   MOLECULAR BIOLOGY AND EVOLUTION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

STRAW: Species TRee Analysis Web server

(2013) Timothy I. Shaw et al.   NUCLEIC ACIDS RESEARCH

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

Targeted sequence capture as a powerful tool for evolutionary analysis1

(2012) Corrinne E. Grover et al.   AMERICAN JOURNAL OF BOTANY

Global biogeography and diversification of palms sheds light on the evolution of tropical lineages. I. Historical biogeography

(2012) William J. Baker et al.   JOURNAL OF BIOGEOGRAPHY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

(2012) M. Lohse et al.   NUCLEIC ACIDS RESEARCH

Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

(2012) Marc T. J. Johnson et al.   PLoS One

Miocene Dispersal Drives Island Radiations in the Palm Tribe Trachycarpeae (Arecaceae)

(2012) Christine D. Bacon et al.   SYSTEMATIC BIOLOGY

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

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Comparative transcriptome and metabolite analysis of oil palm and date palm mesocarp that differ dramatically in carbon partitioning

(2011) F. Bourgis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Sheila Fisher et al.   GENOME BIOLOGY

Assembling the Tree of the Monocotyledons: Plastome Sequence Phylogeny and Evolution of Poales1

(2010) Thomas J. Givnish et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

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

(2010) Bret R. Larget et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

(2010) Jill M Duarte et al.   BMC EVOLUTIONARY BIOLOGY

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Bermuda as an Evolutionary Life Raft for an Ancient Lineage of Endangered Lizards

(2010) Matthew C. Brandley et al.   PLoS One

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes

(2009) Matthew Parks et al.   BMC BIOLOGY

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?

(2009) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Species Trees from Highly Incongruent Gene Trees in Rice

(2009) Karen A. Cranston et al.   SYSTEMATIC BIOLOGY

Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches

(2009) William J. Baker et al.   SYSTEMATIC BIOLOGY

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

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

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

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

Pireella cymbifolia(Pterobryaceae) new to the flora, with comments on sea level and other factors influencing the phytogeography of Bermuda

(2008) Storrs L. Olson   JOURNAL OF BRYOLOGY

The Apicomplexan Whole-Genome Phylogeny: An Analysis of Incongruence among Gene Trees

(2008) C.-H. Kuo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY