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

New insights into the phylogeny, systematics and DNA barcoding of Nemertea

(2014) Sebastian Kvist et al.   INVERTEBRATE SYSTEMATICS

Evaluating Topological Conflict in Centipede Phylogeny Using Transcriptomic Data Sets

(2014) Rosa Fernández et al.   MOLECULAR BIOLOGY AND EVOLUTION

Platyzoan Paraphyly Based on Phylogenomic Data Supports a Noncoelomate Ancestry of Spiralia

(2014) Torsten H. Struck 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

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

SuperQ: Computing Supernetworks from Quartets

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

Morphology of the proboscis ofHubrechtella Juliae(nemertea, pilidiophora): Implications for pilidiophoran monophyly

(2013) Alexey V. Chernyshev et al.   JOURNAL OF MORPHOLOGY

Deep metazoan phylogeny: When different genes tell different stories

(2013) Tetyana Nosenko et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Conserved Genes, Sampling Error, and Phylogenomic Inference

(2013) Ricardo Betancur-R. et al.   SYSTEMATIC BIOLOGY

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea

(2012) Hai-Xia Chen et al.   BMC GENOMICS

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

Modeling Protein Evolution with Several Amino Acid Replacement Matrices Depending on Site Rates

(2012) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY 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

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

(2011) Diego Darriba et al.   BIOINFORMATICS

Disentangling ribbon worm relationships: multi-locus analysis supports traditional classification of the phylum Nemertea

(2011) Sónia C. S. Andrade et al.   CLADISTICS

Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda

(2011) B. M. von Reumont et al.   MOLECULAR BIOLOGY AND EVOLUTION

Let Them Fall Where They May: Congruence Analysis in Massive Phylogenetically Messy Data Sets

(2011) J. W. Leigh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Dating the arthropod tree based on large-scale transcriptome data

(2011) Peter Rehm et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

Phylogenomic analyses unravel annelid evolution

(2011) Torsten H. Struck et al.   NATURE

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

Inferring Species Trees from Gene Trees in a Radiation of California Trapdoor Spiders (Araneae, Antrodiaetidae, Aliatypus)

(2011) Jordan D. Satler et al.   PLoS One

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS

(2010) John E. McCormack et al.   EVOLUTION

Development to metamorphosis of the nemertean pilidium larva

(2010) Svetlana A Maslakova   Frontiers in Zoology

The Invention of the Pilidium Larva in an Otherwise Perfectly Good Spiralian Phylum Nemertea

(2010) S. A. Maslakova   INTEGRATIVE AND COMPARATIVE BIOLOGY

Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships

(2010) K. S. Pick et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

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

(2009) Christoph Bleidorn et al.   BMC EVOLUTIONARY BIOLOGY

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY 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

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Recent developments in the MAFFT multiple sequence alignment program

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

ESTIMATING SPECIES TREES USING MULTIPLE-ALLELE DNA SEQUENCE DATA

(2008) Liang Liu et al.   EVOLUTION

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

(2008) N. Lartillot et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES