Articulating “Archiannelids”: Phylogenomics and Annelid Relationships, with Emphasis on Meiofaunal Taxa

Re-evaluating the phylogeny of Sipuncula through transcriptomics

(2015) Sarah Lemer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A phylogenetic backbone for Bivalvia: an RNA-seq approach

(2015) V. L. Gonzalez et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation

(2015) Christopher E Laumer et al.   eLife

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Phylogeny and systematics of Protodrilidae (Annelida) inferred with total evidence analyses

(2014) Alejandro Martínez et al.   CLADISTICS

Illuminating the Base of the Annelid Tree Using Transcriptomics

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

A Transcriptomic Approach to Ribbon Worm Systematics (Nemertea): Resolving the Pilidiophora Problem

(2014) Sónia C. S. Andrade et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

(2014) Prashant P. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomic analyses of deep gastropod relationships reject Orthogastropoda

(2014) F. Zapata et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenomics of Annelida revisited: a cladistic approach using genome-wide expressed sequence tag data mining and examining the effects of missing data

(2013) Sebastian Kvist et al.   CLADISTICS

SuperQ: Computing Supernetworks from Quartets

(2013) Stefan Grunewald et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Pheromone Evolution, Reproductive Genes, and Comparative Transcriptomics in Mediterranean Earthworms (Annelida, Oligochaeta, Hormogastridae)

(2013) Marta Novo 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

Mitochondrial genomes to the rescue – Diurodrilidae in the myzostomid trap

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

BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions

(2013) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The Impact of Paralogy on Phylogenomic Studies – A Case Study on Annelid Relationships

(2013) Torsten H. Struck   PLoS One

Comparative description of ten transcriptomes of newly sequenced invertebrates and efficiency estimation of genomic sampling in non-model taxa

(2012) Ana Riesgo et al.   Frontiers in Zoology

Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida

(2012) Conrad Helm et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogeny of scale-worms (Aphroditiformia, Annelida), assessed from 18SrRNA, 28SrRNA, 16SrRNA, mitochondrial cytochrome c oxidase subunit I (COI), and morphology

(2012) Erika Norlinder et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Exploiting Gene Families for Phylogenomic Analysis of Myzostomid Transcriptome Data

(2012) Stefanie Hartmann et al.   PLoS One

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

An Early Cambrian stem polychaete with pygidial cirri

(2011) J. Vinther et al.   Biology Letters

Detecting the symplesiomorphy trap: a multigene phylogenetic analysis of terebelliform annelids

(2011) Min Zhong et al.   BMC EVOLUTIONARY BIOLOGY

Direction of evolution within Annelida and the definition of Pleistoannelida

(2011) Torsten H. Struck   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Optimization of preservation and storage time of sponge tissues to obtain quality mRNA for next-generation sequencing

(2011) ANA RIESGO et al.   Molecular Ecology Resources

Phylogenomic analyses unravel annelid evolution

(2011) Torsten H. Struck et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

FrameDP: sensitive peptide detection on noisy matured sequences

(2009) J. Gouzy et al.   BIOINFORMATICS

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

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

Phylogeny of Annelida (Lophotrochozoa): total-evidence analysis of morphology and six genes

(2009) Jan Zrzavý et al.   BMC EVOLUTIONARY BIOLOGY

On the role of character loss in orbiniid phylogeny (Annelida): Molecules vs. morphology

(2009) Christoph Bleidorn et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY