Research graph
References from EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes. Local targets link to admitted publications; unresolved targets remain external evidence.
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities
10.1038/s42003-021-02112-2 · 2021 · External reference
Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes
10.1111/jeu.12691 · 2019 · External reference
Eukaryotic genomes from a global metagenomic dataset illuminate trophic modes and biogeography of ocean plankton
10.1101/2021.07.25.453713 · 2021 · External reference
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
10.1093/nar/25.17.3389 · 1997 · External reference
Professor Thomas Cavalier-Smith FRS FRSC
2021 · External reference
EukRibo: a manually curated eukaryotic 18S rDNA reference database
10.5281/zenodo.6327890 · 2022 · External reference
UniEuk: Time to Speak a Common Language in Protistology!
10.1111/jeu.12414 · 2017 · External reference
Marine microbial metagenomes sampled across space and time
10.1038/sdata.2018.176 · 2018 · External reference
Trimmomatic: a flexible trimmer for Illumina sequence data
10.1093/bioinformatics/btu170 · 2014 · External reference
Tara Oceans studies plankton at planetary scale
10.1126/science.aac5605 · 2015 · External reference
Phylogenomics Places Orphan Protistan Lineages in a Novel Eukaryotic Super-Group
10.1093/gbe/evy014 · 2018 · External reference
The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins
10.1098/rspb.2011.2301 · 2012 · External reference
The New Tree of Eukaryotes
10.1016/j.tree.2019.08.008 · 2020 · External reference
The others: our biased perspective of eukaryotic genomes
10.1016/j.tree.2014.03.006 · 2014 · External reference
A global ocean atlas of eukaryotic genes
10.1038/s41467-017-02342-1 · 2018 · External reference
Development and implementation of high-throughput SNP genotyping in barley
10.1186/1471-2164-10-582 · 2009 · External reference
Seafaring in the 21St Century: The Malaspina 2010 Circumnavigation Expedition
10.1002/lob.10008 · 2015 · External reference
HMMER: biosequence analysis using profile hidden Markov models
2020 · External reference
Phylogenomics: Intersection of Evolution and Genomics
10.1126/science.1086292 · 2003 · External reference
The Pfam protein families database in 2019
10.1093/nar/gky995 · 2019 · External reference
Non-photosynthetic predators are sister to red algae
10.1038/s41586-019-1398-6 · 2019 · External reference
The Gene Ontology Resource: 20 years and still GOing strong
10.1093/nar/gky1055 · 2019 · External reference
PhycoCosm, a comparative algal genomics resource
10.1093/nar/gkaa898 · 2021 · External reference
MycoCosm portal: gearing up for 1000 fungal genomes
10.1093/nar/gkt1183 · 2014 · External reference
phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
10.1128/msystems.00920-20 · 2020 · External reference
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
10.1038/nprot.2013.084 · 2013 · External reference
CAP3: A DNA Sequence Assembly Program
10.1101/gr.9.9.868 · 1999 · External reference
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
10.1093/nar/gky1085 · 2019 · External reference
A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction
10.1016/j.cub.2017.10.051 · 2017 · External reference
Gene Content Evolution in Discobid Mitochondria Deduced from the Phylogenetic Position and Complete Mitochondrial Genome of Tsukubamonas globosa
10.1093/gbe/evu015 · 2014 · External reference
A Holistic Approach to Marine Eco-Systems Biology
10.1371/journal.pbio.1001177 · 2011 · External reference
The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing
10.1371/journal.pbio.1001889 · 2014 · External reference
Embracing Uncertainty in Reconstructing Early Animal Evolution
10.1016/j.cub.2017.08.054 · 2017 · External reference
Comparative genomics reveals the origin of fungal hyphae and multicellularity
10.1038/s41467-019-12085-w · 2019 · External reference
FASconCAT-G: extensive functions for multiple sequence alignment preparations concerning phylogenetic studies
10.1186/s12983-014-0081-x · 2014 · External reference
High spatial resolution global ocean metagenomes from Bio-GO-SHIP repeat hydrography transects
10.1038/s41597-021-00889-9 · 2021 · External reference
Hemimastigophora is a novel supra-kingdom-level lineage of eukaryotes
10.1038/s41586-018-0708-8 · 2018 · External reference
Interactive Tree Of Life (iTOL) v4: recent updates and new developments
10.1093/nar/gkz239 · 2019 · External reference
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
10.1093/bioinformatics/btl158 · 2006 · External reference
A genome-scale phylogeny of the kingdom Fungi
10.1016/j.cub.2021.01.074 · 2021 · External reference
On the optimal trimming of high-throughput mRNA sequence data
10.3389/fgene.2014.00013 · 2014 · External reference
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes
10.1093/molbev/msab199 · 2021 · External reference
The Evolution of Silicon Transport in Eukaryotes
10.1093/molbev/msw209 · 2016 · External reference
Treemmer: a tool to reduce large phylogenetic datasets with minimal loss of diversity
10.1186/s12859-018-2164-8 · 2018 · External reference
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
10.1093/molbev/msaa015 · 2020 · External reference
InterPro in 2019: improving coverage, classification and access to protein sequence annotations
10.1093/nar/gky1100 · 2019 · External reference
The high-throughput gene prediction of more than 1,700 eukaryote genomes using the software package EukMetaSanity
10.1101/2021.07.25.453296 · 2021 · External reference
GFF Utilities: GffRead and GffCompare
10.12688/f1000research.23297.1 · 2020 · External reference
Collaborative data science
2015 · External reference
Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases
10.1093/molbev/msz185 · 2019 · External reference
Using SPAdes De Novo Assembler
10.1002/cpbi.102 · 2020 · External reference
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
10.1093/nar/gks1219 · 2012 · External reference
EMBOSS: The European Molecular Biology Open Software Suite
10.1016/s0168-9525(00)02024-2 · 2000 · External reference
Thomas Cavalier-Smith (1942–2021)
10.1038/d41586-021-01250-1 · 2021 · External reference
The origin and evolution of cell-intrinsic antibacterial defenses in eukaryotes
10.1016/j.gde.2019.09.002 · 2019 · External reference
Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems
10.7554/elife.78129 · 2022 · External reference
EukProt: A database of genome-scale predicted proteins across the diversity of eukaryotes
10.6084/m9.figshare.12417881.v3 · 2022 · External reference
beaplab/EukProt: Initial release to accompany v3 of the EukProt database. GitHub / Zenodo
10.5281/zenodo.7025266 · 2022 · External reference
Thomas Cavalier-Smith (1942–2021)
10.1016/j.cub.2021.07.009 · 2021 · External reference
Obituary for Professor Thomas Cavalier-Smith FRS, FRSC
2021 · External reference
Database resources of the National Center for Biotechnology Information
10.1093/nar/gkz899 · 2020 · External reference
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
10.1093/bioinformatics/btv351 · 2015 · External reference
ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference
10.1371/journal.pbio.3001007 · 2020 · External reference
New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life
10.1093/molbev/msz012 · 2019 · External reference
Phylogenomic insights into the early diversification of fungi
10.1016/j.cub.2022.06.057 · 2022 · External reference
Tara Oceans: towards global ocean ecosystems biology
10.1038/s41579-020-0364-5 · 2020 · External reference
PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
10.1371/journal.pbio.3001365 · 2021 · External reference
Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation
10.1093/sysbio/syx068 · 2018 · External reference
Phylotranscriptomic analysis of the origin and early diversification of land plants
10.1073/pnas.1323926111 · 2014 · External reference
The FAIR Guiding Principles for scientific data management and stewardship
10.1038/sdata.2016.18 · 2016 · External reference
Palpitomonas bilix represents a basal cryptist lineage: insight into the character evolution in Cryptista
10.1038/srep04641 · 2015 · External reference
