A genome-scale phylogeny of the kingdom Fungi

Genome-scale phylogenetic analyses confirm Olpidium as the closest living zoosporic fungus to the non-flagellated, terrestrial fungi

(2021) Ying Chang et al.   Scientific Reports

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

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

101 Dothideomycetes genomes: a test case for predicting lifestyles and emergence of pathogens

(2020) S. Haridas et al.   STUDIES IN MYCOLOGY

Toward a Fully Resolved Fungal Tree of Life

(2020) Timothy Y. James et al.   Annual Review of Microbiology

Phylogenomic Analyses of Non-Dikarya Fungi Supports Horizontal Gene Transfer Driving Diversification of Secondary Metabolism in the Amphibian Gastrointestinal Symbiont, Basidiobolus

(2020) Javier F. Tabima et al.   G3-Genes Genomes Genetics

Feature frequency profile-based phylogenies are inaccurate

(2020) Yuanning Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An investigation of irreproducibility in maximum likelihood phylogenetic inference

(2020) Xing-Xing Shen et al.   Nature Communications

Megaphylogeny resolves global patterns of mushroom evolution

(2019) Torda Varga et al.   Nature Ecology & Evolution

Genome-scale phylogenetics reveals a monophyletic Zoopagales (Zoopagomycota, Fungi)

(2019) William J. Davis et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Model Choice, Missing Data and Taxon Sampling Impact Phylogenomic Inference of Deep Basidiomycota Relationships

(2019) Arun N Prasanna et al.   SYSTEMATIC BIOLOGY

A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium

(2019) Jacob L. Steenwyk et al.   mBio

Notes, outline and divergence times of Basidiomycota

(2019) Mao-Qiang He et al.   FUNGAL DIVERSITY

PHYLOGENETIC CONFLICTS, COMBINABILITY, AND DEEP PHYLOGENOMICS IN PLANTS

(2019) Stephen A Smith et al.   SYSTEMATIC BIOLOGY

Comparative genomics reveals the origin of fungal hyphae and multicellularity

(2019) Enikő Kiss et al.   Nature Communications

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

High-level classification of the Fungi and a tool for evolutionary ecological analyses

(2018) Leho Tedersoo et al.   FUNGAL DIVERSITY

Clarifying the Relationships between Microsporidia and Cryptomycota

(2018) David Bass et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Linking secondary metabolites to gene clusters through genome sequencing of six diverseAspergillusspecies

(2018) Inge Kjærbølling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

(2018) et al.   Genes

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

(2018) Xing-Xing Shen et al.   CELL

Contemporaneous radiations of fungi and plants linked to symbiosis

(2018) François Lutzoni et al.   Nature Communications

A six-gene phylogenetic overview of Basidiomycota and allied phyla with estimated divergence times of higher taxa and a phyloproteomics perspective

(2017) Rui-Lin Zhao et al.   FUNGAL DIVERSITY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

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

Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets

(2017) Xiaofan Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

A genome Tree of Life for the Fungi kingdom

(2017) JaeJin Choi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism

(2017) C Alisha Quandt et al.   eLife

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

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

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

(2016) Joseph W. Spatafora et al.   MYCOLOGIA

OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

(2016) Evgeny M. Zdobnov et al.   NUCLEIC ACIDS RESEARCH

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

(2016) Xing-Xing Shen et al.   G3-Genes Genomes Genetics

Phylogenomics Reveals Convergent Evolution of Lifestyles in Close Relatives of Animals and Fungi

(2015) Guifré Torruella et al.   CURRENT BIOLOGY

Genomics and the making of yeast biodiversity

(2015) Chris Todd Hittinger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Phylogenomic Analyses Indicate that Early Fungi Evolved Digesting Cell Walls of Algal Ancestors of Land Plants

(2015) Ying Chang et al.   Genome Biology and Evolution

Cytology and molecular phylogenetics of Monoblepharidomycetes provide evidence for multiple independent origins of the hyphal habit in the Fungi

(2015) Jaclyn M. Dee et al.   MYCOLOGIA

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

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Torsten H. Struck   Evolutionary Bioinformatics

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

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY 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

Genome and transcriptome sequencing of the halophilic fungus Wallemia ichthyophaga: haloadaptations present and absent

(2013) Janja Zajc et al.   BMC GENOMICS

Shared Signatures of Parasitism and Phylogenomics Unite Cryptomycota and Microsporidia

(2013) Timothy Y. James et al.   CURRENT BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic lineages in Entomophthoromycota

(2013) A.P. Gryganskyi et al.   PERSOONIA

Phylogenomics supports microsporidia as the earliest diverging clade of sequenced fungi

(2012) Salvador Capella-Gutiérrez et al.   BMC BIOLOGY

The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

(2012) Mahajabeen Padamsee et al.   FUNGAL GENETICS AND BIOLOGY

Pruning Rogue Taxa Improves Phylogenetic Accuracy: An Efficient Algorithm and Webservice

(2012) Andre J. Aberer et al.   SYSTEMATIC BIOLOGY

The Fungi: 1, 2, 3 … 5.1 million species?

(2011) Meredith Blackwell   AMERICAN JOURNAL OF BOTANY

A multigene phylogeny of Olpidium and its implications for early fungal evolution

(2011) Satoshi Sekimoto et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic Relationships within the Opisthokonta Based on Phylogenomic Analyses of Conserved Single-Copy Protein Domains

(2011) G. Torruella et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Consistent Phylogenetic Backbone for the Fungi

(2011) I. Ebersberger 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

Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

(2009) Yu Liu et al.   BMC EVOLUTIONARY BIOLOGY

Phylogeny of the "Forgotten" Cellular Slime Mold, Fonticula alba, Reveals a Key Evolutionary Branch within Opisthokonta

(2009) M. W. Brown et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting possibly saturated positions in 18S and 28S sequences and their influence on phylogenetic reconstruction of Annelida (Lophotrochozoa)

(2008) Torsten H. Struck et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic mixture models for proteins

(2008) S. Q. Le et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES