New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data

(2018) Jean-David Grattepanche et al.   BIOESSAYS

Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group

(2018) Matthew W Brown et al.   Genome Biology and Evolution

Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes

(2018) Aaron A. Heiss et al.   Royal Society Open Science

Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids

(2018) Ugo Cenci et al.   BMC BIOLOGY

Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes

(2018) Gordon Lax et al.   NATURE

Between a Pod and a Hard Test: The Deep Evolution of Amoebae

(2017) Seungho Kang et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

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

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

The changing view of eukaryogenesis – fossils, cells, lineages and how they all come together

(2016) Joel B. Dacks et al.   JOURNAL OF CELL SCIENCE

Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista

(2016) Fabien Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Multiple origins of Heliozoa from flagellate ancestors: New cryptist subphylum Corbihelia, superclass Corbistoma, and monophyly of Haptista, Cryptista, Hacrobia and Chromista

(2015) Thomas Cavalier-Smith et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., Two New Alveolate Phyla (Colponemidia nom. nov. and Acavomonidia nom. nov.) and Their Contributions to Reconstructing the Ancestral State of Alveolates and Eukaryotes

(2014) Denis V. Tikhonenkov et al.   PLoS One

Taxon-Rich Phylogenomic Analyses Resolve the Eukaryotic Tree of Life and Reveal the Power of Subsampling by Sites

(2014) Laura A. Katz et al.   SYSTEMATIC BIOLOGY

The others: our biased perspective of eukaryotic genomes

(2014) Javier del Campo et al.   TRENDS IN ECOLOGY & EVOLUTION

The Eukaryotic Tree of Life from a Global Phylogenomic Perspective

(2014) F. Burki   Cold Spring Harbor Perspectives in Biology

Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista

(2014) Akinori Yabuki et al.   Scientific Reports

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh 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

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

Phylogenomics demonstrates that breviate flagellates are related to opisthokonts and apusomonads

(2013) M. W. Brown et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fine Structure of Telonema subtilis Griessmann, 1913: A Flagellate with a Unique Cytoskeletal Structure Among Eukaryotes

(2013) Akinori Yabuki et al.   PROTIST

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

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

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

(2012) Limin Fu et al.   BIOINFORMATICS

Collodictyon--An Ancient Lineage in the Tree of Eukaryotes

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

The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins

(2012) F. Burki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Ultrastructure of Ancyromonas, a Eukaryote without Supergroup Affinities

(2011) Aaron A. Heiss et al.   PROTIST

Microheliella maris (Microhelida ord. n.), an Ultrastructurally Highly Distinctive New Axopodial Protist Species and Genus, and the Unity of Phylum Heliozoa

(2011) Akinori Yabuki et al.   PROTIST

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

(2010) Alexis Criscuolo et al.   BMC EVOLUTIONARY BIOLOGY

Telonemia-specific environmental 18S rDNA PCR reveals unknown diversity and multiple marine-freshwater colonizations

(2010) Jon Bråte et al.   BMC MICROBIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

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

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

Large-Scale Phylogenomic Analyses Reveal That Two Enigmatic Protist Lineages, Telonemia and Centroheliozoa, Are Related to Photosynthetic Chromalveolates

(2009) Fabien Burki et al.   Genome Biology and Evolution

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

Improvement of molecular phylogenetic inference and the phylogeny of Bilateria

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