Complementary combination of multiplex high‐throughput DNA sequencing for molecular phylogeny

Cryptocarya kaengkrachanensis, a new species of Lauraceae from Kaeng Krachan National Park, southwest Thailand

(2020) Meng Zhang et al.   PhytoKeys

Phylogenetic origin of Magnolia pseudokobus (Magnoliaceae), a rare Magnolia extinct in the wild, revealed by chloroplast genome sequencing, genome-wide SNP genotyping and microsatellite analysis

(2020) Shota Sakaguchi et al.   Journal of Forest Research

Museomics for reconstructing historical floristic exchanges: Divergence of stone oaks across Wallacea

(2020) Joeri S. Strijk et al.   PLoS One

Stacks 2: analytical methods for paired‐end sequencing improve RADseq‐based population genomics

(2019) Nicolas C. Rochette et al.   MOLECULAR ECOLOGY

Multiplexed ISSR genotyping by sequencing distinguishes two precious coral species (Anthozoa: Octocorallia: Coralliidae) that share a mitochondrial haplotype

(2019) Kenji Takata et al.   PeerJ

From America to Eurasia: a multigenomes history of the genus Abies

(2018) Svetlana A. Semerikova et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A taxonomic study of Quercus langbianensis complex based on morphology and DNA barcodes of classic and next generation sequences

(2018) Hoang Thi Binh et al.   PhytoKeys

A new species and two new records of Quercus (Fagaceae) from northern Vietnam

(2018) Hoang Thi Binh et al.   PhytoKeys

New infrageneric classification of Abies in light of molecular phylogeny and high diversity in western North America

(2018) Qiao-Ping Xiang et al.   Journal of Systematics and Evolution

Integrated evidence reveals a new species in the ancient blue coral genus Heliopora (Octocorallia)

(2018) Zoe T. Richards et al.   Scientific Reports

Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering

(2017) Richard G. J. Hodel et al.   Scientific Reports

Phylogeny of firs (genus Abies, Pinaceae) based on multilocus nuclear markers (AFLP)

(2016) S. A. Semerikova et al.   RUSSIAN JOURNAL OF GENETICS

Barcoding the kingdom Plantae: new PCR primers forITSregions of plants with improved universality and specificity

(2015) Tao Cheng et al.   Molecular Ecology Resources

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

MIG-seq: an effective PCR-based method for genome-wide single-nucleotide polymorphism genotyping using the next-generation sequencing platform

(2015) Yoshihisa Suyama et al.   Scientific Reports

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

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

(2014) Shadi Shokralla et al.   Molecular Ecology Resources

An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform

(2014) Douglas W Fadrosh et al.   Microbiome

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

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

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants

(2013) Akifumi S. Tanabe et al.   PLoS One

Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation

(2012) Catherine E. Wagner et al.   MOLECULAR ECOLOGY

Multi-locus species delimitation in closely related animals and fungi: one marker is not enough

(2012) JULIAN R. DUPUIS et al.   MOLECULAR ECOLOGY

The seven deadly sins of DNA barcoding

(2012) R. A. Collins et al.   Molecular Ecology Resources

Coalescent-based species delimitation in an integrative taxonomy

(2012) Matthew K. Fujita et al.   TRENDS IN ECOLOGY & EVOLUTION

Kakusan4 and Aminosan: two programs for comparing nonpartitioned, proportional and separate models for combined molecular phylogenetic analyses of multilocus sequence data

(2011) AKIFUMI S. TANABE   Molecular Ecology Resources

Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context

(2011) Érika Aguirre-Planter et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama

(2009) W. J. Kress et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A DNA barcode for land plants

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