Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

Standardized benchmarking in the quest for orthologs

(2016) Adrian M Altenhoff et al.   NATURE METHODS

A molecular palaeobiological exploration of arthropod terrestrialization

(2016) Jesus Lozano-Fernandez et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction

(2016) Rosa Fernández et al.   SYSTEMATIC BIOLOGY

Spiralian Phylogeny Informs the Evolution of Microscopic Lineages

(2015) Christopher E. Laumer et al.   CURRENT BIOLOGY

Phylogenetic relationships between living and fossil spinicaudatan taxa (Branchiopoda Spinicaudata): reconsidering the evidence

(2015) Timothy I. Astrop et al.   JOURNAL OF CRUSTACEAN BIOLOGY

The forest for the trees: evaluating molecular phylogenies with an emphasis on higher-level Decapoda

(2015) Laura Timm et al.   JOURNAL OF CRUSTACEAN BIOLOGY

Evolutionary systematics of the Australian Cyzicidae (Crustacea, Branchiopoda, Spinicaudata) with the description of a new genus

(2015) Martin Schwentner et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

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

Phylogenomic Analysis of Spiders Reveals Nonmonophyly of Orb Weavers

(2014) Rosa Fernández et al.   CURRENT BIOLOGY

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

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

A transcriptome approach to ecdysozoan phylogeny

(2014) Janus Borner et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

Onychocaudata (Branchiopoda: Diplostraca), a new high-level taxon in branchiopod systematics

(2013) Jørgen Olesen et al.   JOURNAL OF CRUSTACEAN BIOLOGY

Evolutionary systematics of the AustralianEocyzicusfauna (Crustacea: Branchiopoda: Spinicaudata) reveals hidden diversity and phylogeographic structure

(2013) Martin Schwentner et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

(2013) Emiliano Dell’Ampio et al.   MOLECULAR BIOLOGY 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

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

(2013) Adrian M. Altenhoff et al.   PLoS One

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

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Arthropod fossil data increase congruence of morphological and molecular phylogenies

(2013) David A. Legg et al.   Nature Communications

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Evolutionary Shift from Fighting to Foraging in Blind Cavefish through Changes in the Serotonin Network

(2012) Yannick Elipot et al.   CURRENT BIOLOGY

Improving Phylogenetic Inference with a Semiempirical Amino Acid Substitution Model

(2012) S. Zoller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny

(2012) Todd H. Oakley et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mitogenomic analysis of decapod crustacean phylogeny corroborates traditional views on their relationships

(2012) Hong Shen et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Accounting For Alignment Uncertainty in Phylogenomics

(2012) Martin Wu et al.   PLoS One

Serine Codon-Usage Bias in Deep Phylogenomics: Pancrustacean Relationships as a Case Study

(2012) Omar Rota-Stabelli et al.   SYSTEMATIC BIOLOGY

A new view of insect–crustacean relationships II. Inferences from expressed sequence tags and comparisons with neural cladistics

(2011) David R. Andrew   ARTHROPOD STRUCTURE & DEVELOPMENT

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

(2011) Seth M. Bybee et al.   Genome Biology and Evolution

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

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

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

Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences

(2010) Jerome C. Regier et al.   NATURE

A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata

(2010) O. Rota-Stabelli et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Higher-level crustacean phylogeny: Consensus and conflicting hypotheses

(2009) Ronald A. Jenner   ARTHROPOD STRUCTURE & DEVELOPMENT

Arthropod phylogeny: An overview from the perspectives of morphology, molecular data and the fossil record

(2009) Gregory D. Edgecombe   ARTHROPOD STRUCTURE & DEVELOPMENT

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

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

Eumalacostracan phylogeny and total evidence: limitations of the usual suspects

(2009) Ronald A Jenner et al.   BMC EVOLUTIONARY BIOLOGY

Evolutionary morphology of the circulatory system in Peracarida (Malacostraca; Crustacea)

(2009) Christian S. Wirkner et al.   CLADISTICS

Evolutionary transitions among dioecy, androdioecy and hermaphroditism in limnadiid clam shrimp (Branchiopoda: Spinicaudata)

(2009) S. C. WEEKS et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Phylogeny of Spinicaudata (Branchiopoda, Crustacea) based on three molecular markers – An Australian origin for Limnadopsis

(2009) Martin Schwentner 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

Phylogeny of Thalassinidea (Crustacea, Decapoda) inferred from three rDNA sequences: implications for morphological evolution and superfamily classification

(2008) L. M. Tsang et al.   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH