The Utility of Genome Skimming for Phylogenomic Analyses as Demonstrated for Glycerid Relationships (Annelida, Glyceridae)

Metagenome Skimming of Insect Specimen Pools: Potential for Comparative Genomics

(2015) Benjamin Linard et al.   Genome Biology and Evolution

The complete mitochondrial genome of the polychaete,Goniada japonica(Phyllodocida, Goniadidae)

(2015) Xinghan Chen et al.   Mitochondrial DNA

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

(2015) Alex Crampton-Platt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic community ecology of soil biodiversity using mitochondrial metagenomics

(2015) Carmelo Andújar et al.   MOLECULAR ECOLOGY

Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida)

(2015) Yuanning Li et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata

(2015) M. Teresa Aguado et al.   Scientific Reports

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Phylogenomic Analysis of Spiders Reveals Nonmonophyly of Orb Weavers

(2014) Rosa Fernández et al.   CURRENT BIOLOGY

A Polychaete’s Powerful Punch: Venom Gland Transcriptomics of Glycera Reveals a Complex Cocktail of Toxin Homologs

(2014) Björn M. von Reumont et al.   Genome Biology and Evolution

Illuminating the Base of the Annelid Tree Using Transcriptomics

(2014) Anne Weigert et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

leeHom: adaptor trimming and merging for Illumina sequencing reads

(2014) Gabriel Renaud et al.   NUCLEIC ACIDS RESEARCH

A cost-effective straightforward protocol for shotgun Illumina libraries designed to assemble complete mitogenomes from non-model species

(2014) Marie-Ka Tilak et al.   Conservation Genetics Resources

Quo Vadis Venomics? A Roadmap to Neglected Venomous Invertebrates

(2014) Bjoern von Reumont et al.   Toxins

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

(2014) Steve Hoffmann et al.   GENOME BIOLOGY

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers

(2013) Gabriel Renaud et al.   BIOINFORMATICS

The complete mitochondrial genome of a turbinid vetigastropod from MiSeq Illumina sequencing of genomic DNA and steps towards a resolved gastropod phylogeny

(2013) S.T. Williams et al.   GENE

Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes

(2013) Nimrod D. Rubinstein et al.   Genome Biology and Evolution

DAMBE5: A Comprehensive Software Package for Data Analysis in Molecular Biology and Evolution

(2013) Xuhua Xia   MOLECULAR BIOLOGY AND EVOLUTION

Mitochondrial genomes to the rescue – Diurodrilidae in the myzostomid trap

(2013) Anja Golombek et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae)

(2013) Fidel Botero-Castro et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads—a baiting and iterative mapping approach

(2013) Christoph Hahn et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

Mitochondrial genome diversity and population structure of the giant squid Architeuthis: genetics sheds new light on one of the most enigmatic marine species

(2013) I. Winkelmann et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

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

(2012) Y. Peng et al.   BIOINFORMATICS

Next generation sequencing and comparative analyses of Xenopus mitogenomes

(2012) Rhiannon E Lloyd et al.   BMC GENOMICS

Molecular anatomy of tunicate senescence: reversible function of mitochondrial and nuclear genes associated with budding cycles

(2012) K. Kawamura et al.   DEVELOPMENT

Mitochondrial DNA of Clathrina clathrus (Calcarea, Calcinea): Six Linear Chromosomes, Fragmented rRNAs, tRNA Editing, and a Novel Genetic Code

(2012) Dennis V. Lavrov et al.   MOLECULAR BIOLOGY AND EVOLUTION

MITOS: Improved de novo metazoan mitochondrial genome annotation

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

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Complex cocktails: the evolutionary novelty of venoms

(2012) Nicholas R. Casewell et al.   TRENDS IN ECOLOGY & EVOLUTION

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial Genomes Reveal Slow Rates of Molecular Evolution and the Timing of Speciation in Beavers (Castor), One of the Largest Rodent Species

(2011) Susanne Horn et al.   PLoS One

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

(2011) Linnéa Smeds et al.   PLoS One

Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

(2010) P. A. Morin et al.   GENOME RESEARCH

Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products

(2010) Tomislav Maricic et al.   PLoS One

Evidence for a role of bathymetry and emergence in speciation in the genus Glycera (Glyceridae, Polychaeta) from the deep Eastern Weddell Sea

(2010) Myriam Schüller   POLAR BIOLOGY

Group II Introns: Mobile Ribozymes that Invade DNA

(2010) A. M. Lambowitz et al.   Cold Spring Harbor Perspectives in Biology

The Toxicogenomic Multiverse: Convergent Recruitment of Proteins Into Animal Venoms

(2009) Bryan G. Fry et al.   Annual Review of Genomics and Human Genetics

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

On the phylogenetic position of Myzostomida: Can 77 genes get it wrong?

(2009) Christoph Bleidorn et al.   BMC EVOLUTIONARY BIOLOGY

Mitochondrial genome sequence and gene order of Sipunculus nudus give additional support for an inclusion of Sipuncula into Annelida

(2009) Adina Mwinyi et al.   BMC GENOMICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Phylogeny of the bristle worm family Eunicidae (Eunicida, Annelida) and the phylogenetic utility of noncongruent 16S, COI and 18S in combined analyses

(2009) Joana Zanol et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures

(2009) Steve Hoffmann et al.   PLoS Computational Biology

Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa)

(2008) Torsten H. Struck et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Group II Introns Break New Boundaries: Presence in a Bilaterian's Genome

(2008) Yvonne Vallès et al.   PLoS One