Plastome phylogenomics of sugarcane and relatives confirms the segregation of the genus Tripidium (Poaceae: Andropogoneae)

Plastid phylogenomics resolves infrafamilial relationships of the Styracaceae and sheds light on the backbone relationships of the Ericales

(2018) Minghui Yan et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evolutionary dynamism in bryophytes: Phylogenomic inferences confirm rapid radiation in the moss family Funariaceae

(2018) Rafael Medina et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

(2018) Jeffery M. Saarela et al.   PeerJ

Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics

(2017) Shu-Dong Zhang et al.   NEW PHYTOLOGIST

Complete Chloroplast Genomes of Erianthus arundinaceus and Miscanthus sinensis: Comparative Genomics and Evolution of the Saccharum Complex

(2017) Shin-ichi Tsuruta et al.   PLoS One

Phylogenomics of Andropogoneae (Panicoideae: Poaceae) of Mainland Southeast Asia

(2017) Watchara Arthan et al.   SYSTEMATIC BOTANY

A New Allopolyploid Species of Saccharum (Poaceae ‐ Andropogoneae) from South America, with Notes on its Cytogenetics

(2017) Cassiano A. D. Welker et al.   SYSTEMATIC BOTANY

A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications

(2017) Robert J. Soreng et al.   Journal of Systematics and Evolution

Strongly asymmetric hybridization barriers shape the origin of a new polyploid species and its hybrid ancestor

(2016) Mario Vallejo-Marín et al.   AMERICAN JOURNAL OF BOTANY

Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes

(2016) Michael R. McKain et al.   BIOINFORMATICS

Evolutionary relationships in Panicoid grasses based on plastome phylogenomics (Panicoideae; Poaceae)

(2016) Sean V. Burke et al.   BMC PLANT BIOLOGY

Multilocus phylogeny and phylogenomics of Eriochrysis P. Beauv. (Poaceae–Andropogoneae): Taxonomic implications and evidence of interspecific hybridization

(2016) Cassiano A.D. Welker et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis

(2016) Lakshmi Attigala et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomic and structural analyses of 18 complete plastomes across nearly all families of early-diverging eudicots, including an angiosperm-wide analysis of IR gene content evolution

(2016) Yanxia Sun et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Complete chloroplast genomes of Saccharum spontaneum, Saccharum officinarum and Miscanthus floridulus (Panicoideae: Andropogoneae) reveal the plastid view on sugarcane origins

(2016) Dyfed Lloyd Evans et al.   SYSTEMATICS AND BIODIVERSITY

Phylogenetic analysis of Saccharum s.l . (Poaceae; Andropogoneae), with emphasis on the circumscription of the South American species

(2015) Cassiano A. D. Welker et al.   AMERICAN JOURNAL OF BOTANY

Resolving deep relationships of PACMAD grasses: a phylogenomic approach

(2015) Joseph L. Cotton et al.   BMC PLANT BIOLOGY

Complete chloroplast genomes of two Miscanthus species

(2015) Gyoungju Nah et al.   Mitochondrial DNA Part A

Phylogenetics of Panicoideae (Poaceae) based on chloroplast and nuclear DNA sequences

(2015) Atchara Teerawatananon et al.   TELOPEA

Biogeography and phylogenomics of New World Bambusoideae (Poaceae), revisited

(2014) Sean V. Burke et al.   AMERICAN JOURNAL OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Comparative Analysis of Miscanthus and Saccharum Reveals a Shared Whole-Genome Duplication but Different Evolutionary Fates

(2014) C. Kim et al.   PLANT CELL

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Allopolyploidy, diversification, and the Miocene grassland expansion

(2014) Matt C. Estep et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sugarcane (Saccharum X officinarum): A Reference Study for the Regulation of Genetically Modified Cultivars in Brazil

(2011) Adriana Cheavegatti-Gianotto et al.   Tropical Plant Biology

A taxonomic revision of Miscanthus s.l. (Poaceae) from China

(2010) QIAN SUN et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS