OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity

Ten years of collaborative progress in the Quest for Orthologs

(2021) Benjamin Linard et al.   MOLECULAR BIOLOGY AND EVOLUTION

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

(2021) Mosè Manni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mouse Genome Informatics (MGI): latest news from MGD and GXD

(2021) Martin Ringwald et al.   MAMMALIAN GENOME

GenBank

(2021) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms

(2021) Gloria I Giraldo-Calderón et al.   Current Opinion in Insect Science

LEMMI: A continuous benchmarking platform for metagenomics classifiers

(2020) Mathieu Seppey et al.   GENOME RESEARCH

Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench

(2020) D M Emms et al.   Genome Biology and Evolution

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

OrthoDB in 2020: evolutionary and functional annotations of orthologs

(2020) Evgeny M Zdobnov et al.   NUCLEIC ACIDS RESEARCH

MMseqs2 desktop and local web server app for fast, interactive sequence searches

(2019) M Mirdita et al.   BIOINFORMATICS

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

(2019) Davide Heller et al.   BMC BIOINFORMATICS

SonicParanoid: fast, accurate, and easy orthology inference

(2018) Salvatore Cosentino et al.   BIOINFORMATICS

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

FlyBase 2.0: the next generation

(2018) Jim Thurmond et al.   NUCLEIC ACIDS RESEARCH

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

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

(2014) Evgenia V. Kriventseva et al.   NUCLEIC ACIDS RESEARCH

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders

(2014) Joanna S. Amberger et al.   NUCLEIC ACIDS RESEARCH

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters

(2012) Akihiro Nakaya et al.   NUCLEIC ACIDS RESEARCH

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS