Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of different reconstruction methods

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics of Lophotrochozoa with Consideration of Systematic Error

(2016) Kevin M. Kocot et al.   SYSTEMATIC BIOLOGY

Bone-eating Osedax worms lived on Mesozoic marine reptile deadfalls

(2015) S. Danise et al.   Biology Letters

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

A Dwarf Male Reversal in Bone-Eating Worms

(2015) Greg W. Rouse et al.   CURRENT BIOLOGY

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

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

Coalescent methods for estimating species trees from phylogenomic data

(2015) Liang Liu et al.   Journal of Systematics and Evolution

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

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Resolves a Spider Backbone Phylogeny and Rejects a Prevailing Paradigm for Orb Web Evolution

(2014) Jason E. Bond et al.   CURRENT BIOLOGY

Illuminating the Base of the Annelid Tree Using Transcriptomics

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

Species tree estimation of North American chorus frogs (Hylidae: Pseudacris) with parallel tagged amplicon sequencing

(2014) Lisa N. Barrow et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

The multispecies coalescent model and land plant origins: a reply to Springer and Gatesy

(2014) Bojian Zhong et al.   TRENDS IN PLANT SCIENCE

MICROEVOLUTIONARY PROCESSES GENERATE PHYLOGENOMIC DISCORDANCE AT ANCIENT DIVERGENCES

(2013) Jeffrey C. Oliver   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

STRAW: Species TRee Analysis Web server

(2013) Timothy I. Shaw et al.   NUCLEIC ACIDS RESEARCH

Concatenation versus coalescence versus "concatalescence"

(2013) J. Gatesy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reply to Gatesy and Springer: The multispecies coalescent model can effectively handle recombination and gene tree heterogeneity

(2013) S. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bone-eating worms from the Antarctic: the contrasting fate of whale and wood remains on the Southern Ocean seafloor

(2013) A. G. Glover et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Origin of land plants using the multispecies coalescent model

(2013) Bojian Zhong et al.   TRENDS IN PLANT SCIENCE

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Is Recombination a Problem for Species-Tree Analyses?

(2012) Hayley C. Lanier et al.   SYSTEMATIC BIOLOGY

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

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

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

New Perspectives on the Ecology and Evolution of Siboglinid Tubeworms

(2011) Ana Hilário et al.   PLoS One

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

Endosymbionts of Siboglinum fiordicum and the Phylogeny of Bacterial Endosymbionts in Siboglinidae (Annelida)

(2010) Daniel J. Thornhill et al.   BIOLOGICAL BULLETIN

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

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

(2009) Ingo Ebersberger et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY

The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference

(2009) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Additional molecular support for the new chordate phylogeny

(2008) Frédéric Delsuc et al.   GENESIS

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE