Phylogenomic analyses recover a clade of large-bodied decapodiform cephalopods

New methods to calculate concordance factors for phylogenomic datasets

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic reconstruction based on synteny block and gene adjacencies

(2020) Guénola Drillon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Scalable Empirical Mixture Models That Account for Across-Site Compositional Heterogeneity

(2020) Dominik Schrempf et al.   MOLECULAR BIOLOGY AND EVOLUTION

Symbiotic organs shaped by distinct modes of genome evolution in cephalopods

(2019) Mahdi Belcaid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Relative Importance of Modeling Site Pattern Heterogeneity Versus Partition-Wise Heterotachy in Phylogenomic Inference

(2019) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Synteny footprints provide clearer phylogenetic signal than sequence data for prokaryotic classification

(2019) Gur Sevillya et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Prevalence and Impact of Model Violations in Phylogenetic Analysis

(2019) Suha Naser-Khdour et al.   Genome Biology and Evolution

PhyloMAd: efficient assessment of phylogenomic model adequacy

(2018) David A Duchêne et al.   BIOINFORMATICS

Updated molecular phylogeny of the squid family Ommastrephidae: Insights into the evolution of spawning strategies

(2018) M. Cecilia Pardo-Gandarillas et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Assessing the utility of transcriptome data for inferring phylogenetic relationships among coleoid cephalopods

(2018) Annie R. Lindgren et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

How Well Does Your Phylogenetic Model Fit Your Data?

(2018) Daisy A Shepherd et al.   SYSTEMATIC BIOLOGY

Revisiting the phylogeny of Cephalopoda using complete mitochondrial genomes

(2017) Juan E. Uribe et al.   JOURNAL OF MOLLUSCAN STUDIES

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Whole mitochondrial genome of the Ram’s Horn Squid shines light on the phylogenetic position of the monotypic order Spirulida (Haeckel, 1896)

(2017) Jan M. Strugnell et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

Global proliferation of cephalopods

(2016) Zoë A. Doubleday et al.   CURRENT BIOLOGY

Computing the Internode Certainty and Related Measures from Partial Gene Trees

(2016) Kassian Kobert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Reply to Halanych et al.: Ctenophore misplacement is corroborated by independent datasets

(2016) Davide Pisani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Miscues misplace sponges

(2016) Kenneth M. Halanych et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

The octopus genome and the evolution of cephalopod neural and morphological novelties

(2015) Caroline B. Albertin et al.   NATURE

Genomic data do not support comb jellies as the sister group to all other animals

(2015) Davide Pisani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Can We Identify Genes with Increased Phylogenetic Reliability?

(2015) Vinson P. Doyle et al.   SYSTEMATIC BIOLOGY

World Squid Fisheries

(2015) Alexander I. Arkhipkin et al.   Reviews in Fisheries Science & Aquaculture

SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity

(2014) C. N. Magnan et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

TreSpEx–-Detection of Misleading Signal in Phylogenetic Reconstructions Based on Tree Information

(2014) Torsten H. Struck   Evolutionary Bioinformatics

The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review

(2014) A. Louise Allcock et al.   JOURNAL OF NATURAL HISTORY

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

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

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit

(2014) Jeremy M. Brown   SYSTEMATIC BIOLOGY

PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics

(2013) Kevin M. Kocot et al.   Evolutionary Bioinformatics

New molecular phylogeny of the squids of the family Loliginidae with emphasis on the genus Doryteuthis Naef, 1912: Mitochondrial and nuclear sequences indicate the presence of cryptic species in the southern Atlantic Ocean

(2013) João Bráullio de Luna Sales 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

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

A multi-gene phylogeny of Cephalopoda supports convergent morphological evolution in association with multiple habitat shifts in the marine environment

(2012) Annie R Lindgren et al.   BMC EVOLUTIONARY BIOLOGY

Cyclonic eddies reveal Oegopsida squid egg balloon masses in the Agulhas Current, South Africa

(2011) M J Roberts et al.   AFRICAN JOURNAL OF MARINE SCIENCE

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

(2011) Min Zhong et al.   BMC EVOLUTIONARY BIOLOGY

Acoelomorph flatworms are deuterostomes related to Xenoturbella

(2011) Hervé Philippe et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

What can the mitochondrial genome reveal about higher-level phylogeny of the molluscan class Cephalopoda?

(2011) A. LOUISE ALLCOCK et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Molecular inference of phylogenetic relationships among Decapodiformes (Mollusca: Cephalopoda) with special focus on the squid Order Oegopsida

(2010) Annie R. Lindgren   MOLECULAR PHYLOGENETICS AND EVOLUTION

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

HaMStR: Profile hidden markov model based search for orthologs in ESTs

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS