Plastid genomes and deep relationships among the commelinid monocot angiosperms

Targeted enrichment strategies for next-generation plant biology

(2012) Richard Cronn et al.   AMERICAN JOURNAL OF BOTANY

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

(2012) P. Roxanne Steele et al.   AMERICAN JOURNAL OF BOTANY

Phylogenetic Analysis of the Plastid Inverted Repeat for 244 Species: Insights into Deeper-Level Angiosperm Relationships from a Long, Slowly Evolving Sequence Region

(2011) Michael J. Moore et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Reconciling Gene and Genome Duplication Events: Using Multiple Nuclear Gene Families to Infer the Phylogeny of the Aquatic Plant Family Pontederiaceae

(2011) Rob W. Ness et al.   MOLECULAR BIOLOGY AND EVOLUTION

Spurious 99% bootstrap and jackknife support for unsupported clades

(2011) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

High-Throughput Sequencing of Three Lemnoideae (Duckweeds) Chloroplast Genomes from Total DNA

(2011) Wenqin Wang et al.   PLoS One

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

A Functional Phylogenomic View of the Seed Plants

(2011) Ernest K. Lee et al.   PLoS Genetics

Assembling the Angiosperm Tree of Life: Progress and Future Prospects

(2010) Douglas E. Soltis et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

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

Evolutionary History of the Monocot Flower1

(2010) Margarita V. Remizowa et al.   ANNALS OF THE MISSOURI BOTANICAL GARDEN

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae

(2010) Fu-Hui Wu et al.   BMC PLANT BIOLOGY

Branch support via resampling: an empirical study

(2010) John V. Freudenstein et al.   CLADISTICS

SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information

(2010) Gaurav Vaidya et al.   CLADISTICS

Implications of the Plastid Genome Sequence of Typha (Typhaceae, Poales) for Understanding Genome Evolution in Poaceae

(2010) Mary M. Guisinger et al.   JOURNAL OF MOLECULAR EVOLUTION

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

(2010) K. S. Pick et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.)

(2010) Meng Yang et al.   PLoS One

Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots

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

Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

(2010) J. Gordon Burleigh et al.   SYSTEMATIC BIOLOGY

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

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

(2009) Matthew Parks et al.   BMC BIOLOGY

An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III

(2009)   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Molecular Markers and Concepts of Plant Evolutionary Relationships: Progress, Promise, and Future Prospects

(2009) Douglas E. Soltis et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS

Rosid radiation and the rapid rise of angiosperm-dominated forests

(2009) H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Concatenated Analysis Sheds Light on Early Metazoan Evolution and Fuels a Modern “Urmetazoon” Hypothesis

(2009) Bernd Schierwater et al.   PLOS BIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

(2008) Jeffery M. Saarela et al.   Botany

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

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

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

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Phylogenetic utility of ycf1 in orchids: a plastid gene more variable than matK

(2008) Kurt M. Neubig et al.   PLANT SYSTEMATICS AND EVOLUTION

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY