Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

The evolutionary history of ferns inferred from 25 low-copy nuclear genes

(2015) C. J. Rothfels et al.   AMERICAN JOURNAL OF BOTANY

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Monocot fossils suitable for molecular dating analyses

(2015) William J. D. Iles et al.   BOTANICAL JOURNAL OF THE LINNEAN SOCIETY

Evolution of petaloidy in the zingiberales: An assessment of the relationship between ultrastructure and gene expression patterns

(2015) Ana Maria Rocha de Almeida et al.   DEVELOPMENTAL DYNAMICS

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2014) S. Mirarab et al.   SCIENCE

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

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

Resolving ancient radiations: can complete plastid gene sets elucidate deep relationships among the tropical gingers (Zingiberales)?

(2013) Craig F. Barrett et al.   ANNALS OF BOTANY

“A draft Musa balbisiana genome sequence for molecular genetics in polyploid, inter- and intra-specific Musa hybrids”

(2013) Mark W Davey et al.   BMC GENOMICS

Molecular Evolution and Patterns of Duplication in the SEP/AGL6-Like Lineage of the Zingiberales: A Proposed Mechanism for Floral Diversification

(2013) Roxana Yockteng et al.   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

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

Concatenation versus coalescence versus "concatalescence"

(2013) J. Gatesy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer

(2012) Pierre Peterlongo et al.   BMC BIOINFORMATICS

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

(2012) Ke Bi et al.   BMC GENOMICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants

(2012) Angélique D’Hont et al.   NATURE

Phytolith variability in Zingiberales: A tool for the reconstruction of past tropical vegetation

(2012) Stephanie T. Chen et al.   PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY

Long identical multispecies elements in plant and animal genomes

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

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

Phylogenetic Relationships and Evolution in the Strelitziaceae (Zingiberales)

(2012) Glynis V. Cron et al.   SYSTEMATIC BOTANY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genotype and SNP calling from next-generation sequencing data

(2011) Rasmus Nielsen et al.   NATURE REVIEWS GENETICS

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

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

(2010) A. McKenna et al.   GENOME RESEARCH

Molecular phylogeny and systematics of the banana family (Musaceae) inferred from multiple nuclear and chloroplast DNA fragments, with a special reference to the genus Musa

(2010) Lin-Feng Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Evidence for the involvement of GLOBOSA-like gene duplications and expression divergence in the evolution of floral morphology in the Zingiberales

(2010) Madelaine E. Bartlett et al.   NEW PHYTOLOGIST

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing

(2009) Emily Hodges et al.   Nature Protocols

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY

Ancient Rapid Radiations of Insects: Challenges for Phylogenetic Analysis

(2007) James B. Whitfield et al.   Annual Review of Entomology