PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies

Ten years of collaborative progress in the Quest for Orthologs

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

Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations

(2021) Verónica Mixão et al.   DNA RESEARCH

Gene gain and loss across the metazoan tree of life

(2020) Rosa Fernández et al.   Nature Ecology & Evolution

Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum

(2020) Rosa Fernández et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Quest for Orthologs benchmark service and consensus calls in 2020

(2020) Adrian M Altenhoff et al.   NUCLEIC ACIDS RESEARCH

MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life

(2020) Uciel Chorostecki et al.   NUCLEIC ACIDS RESEARCH

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

(2020) Nicolas Comte et al.   BIOINFORMATICS

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

(2020) Claude Rispe et al.   BMC BIOLOGY

Phylogenomics identifies an ancestral burst of gene duplications predating the diversification of aphidomorpha

(2019) Irene Julca et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parental origin of the allotetraploid tobacco Nicotiana benthamiana

(2019) Matteo Schiavinato et al.   PLANT JOURNAL

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events

(2018) Irene Julca et al.   BMC BIOLOGY

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

Genome-wide signatures of complex introgression and adaptive evolution in the big cats

(2017) Henrique V. Figueiró et al.   Science Advances

Expansion of Signal Transduction Pathways in Fungi by Extensive Genome Duplication

(2016) Luis M. Corrochano et al.   CURRENT BIOLOGY

Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life

(2016) Antonio Figueras et al.   DNA RESEARCH

Genome, Transcriptome, and Functional Analyses ofPenicillium expansumProvide New Insights Into Secondary Metabolism and Pathogenicity

(2015) Ana-Rosa Ballester et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

TheSolanum commersoniiGenome Sequence Provides Insights into Adaptation to Stress Conditions and Genome Evolution of Wild Potato Relatives

(2015) Riccardo Aversano et al.   PLANT CELL

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

(2015) Solenn Patalano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts

(2015) Guillaume Morel et al.   Scientific Reports

Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage

(2015) Marina Marcet-Houben et al.   PLOS BIOLOGY

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

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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The GOA database: Gene Ontology annotation updates for 2015

(2014) Rachael P. Huntley et al.   NUCLEIC ACIDS RESEARCH

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima

(2014) Ariel D. Chipman et al.   PLOS BIOLOGY

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

(2013) Juliane C. Dohm et al.   NATURE

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information

(2011) T. Schmitt et al.   BRIEFINGS IN BIOINFORMATICS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

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

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY