Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample

Capturing protein-coding genes across highly divergent species

(2016) Chenhong Li et al.   BIOTECHNIQUES

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing

(2014) Guillaume Besnard et al.   COMPTES RENDUS BIOLOGIES

Angiosperm Phylogeny Based on 18S/26S rDNA Sequence Data: Constructing a Large Data Set Using Next-Generation Sequence Data

(2014) Vitor H. Maia et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

Bulk De Novo Mitogenome Assembly from Pooled Total DNA Elucidates the Phylogeny of Weevils (Coleoptera: Curculionoidea)

(2014) Conrad P.D.T. Gillett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiplex sequencing of pooled mitochondrial genomes—a crucial step toward biodiversity analysis using mito-metagenomics

(2014) Min Tang et al.   NUCLEIC ACIDS RESEARCH

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

(2014) J. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity

(2014) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Insect Mitochondrial Genomics: Implications for Evolution and Phylogeny

(2013) Stephen L. Cameron   Annual Review of Entomology

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

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

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

A comparative analysis of complete mitochondrial genomes among Hexapoda

(2013) Sabrina Simon et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny

(2013) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Rare Failures of DNA Bar Codes to Separate Morphologically Distinct Species in a Biodiversity Survey of Iberian Leaf Beetles

(2013) Andrés Baselga et al.   PLoS One

Building the Coleoptera tree-of-life for >8000 species: composition of public DNA data and fit with Linnaean classification

(2013) LADISLAV BOCAK et al.   SYSTEMATIC ENTOMOLOGY

One hundred and one new species of Trigonopterus weevils from New Guinea

(2013) Alexander Riedel et al.   ZooKeys

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

Qualimap: evaluating next-generation sequencing alignment data

(2012) Fernando García-Alcalde et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

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

(2012) M. Kearse et al.   BIOINFORMATICS

Reference databases for taxonomic assignment in metagenomics

(2012) M. Santamaria et al.   BRIEFINGS IN BIOINFORMATICS

Using Tablet for visual exploration of second-generation sequencing data

(2012) I. Milne et al.   BRIEFINGS IN BIOINFORMATICS

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding

(2012) H. R. TAYLOR et al.   Molecular Ecology Resources

Phylogenetically informative rearrangements in mitochondrial genomes of Coleoptera, and monophyly of aquatic elateriform beetles (Dryopoidea)

(2012) Martijn J.T.N. Timmermans et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genetic aspects of mitochondrial genome evolution

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Insect phylogenomics: results, problems and the impact of matrix composition

(2012) H. O. Letsch 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

Mapping the biosphere: exploring species to understand the origin, organization and sustainability of biodiversity

(2012) Q. D. Wheeler et al.   SYSTEMATICS AND BIODIVERSITY

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Ramping up biodiversity discovery via online quantum contributions

(2011) David R. Maddison et al.   TRENDS IN ECOLOGY & EVOLUTION

Evolutionary informatics: unifying knowledge about the diversity of life

(2011) Cynthia S. Parr et al.   TRENDS IN ECOLOGY & EVOLUTION

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Guild-specific patterns of species richness and host specialization in plant-herbivore food webs from a tropical forest

(2010) Vojtech Novotny et al.   JOURNAL OF ANIMAL ECOLOGY

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises

(2010) S. CREER et al.   MOLECULAR ECOLOGY

Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

(2010) M. J. T. N. Timmermans et al.   NUCLEIC ACIDS RESEARCH

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Accelerated Species Inventory on Madagascar Using Coalescent-Based Models of Species Delineation

(2009) Michael T. Monaghan et al.   SYSTEMATIC BIOLOGY

Phylogenetic beta diversity: linking ecological and evolutionary processes across space in time

(2008) Catherine H. Graham et al.   ECOLOGY LETTERS