Gene gain and loss across the metazoan tree of life

A New Spiralian Phylogeny Places the Enigmatic Arrow Worms among Gnathiferans

(2019) Ferdinand Marlétaz et al.   CURRENT BIOLOGY

Revisiting metazoan phylogeny with genomic sampling of all phyla

(2019) Christopher E. Laumer et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Reconstruction of the ancestral metazoan genome reveals an increase in genomic novelty

(2018) Jordi Paps et al.   Nature Communications

Gene family innovation, conservation and loss on the animal stem lineage

(2018) Daniel J Richter et al.   eLife

Early metazoan cell type diversity and the evolution of multicellular gene regulation

(2018) Arnau Sebé-Pedrós et al.   Nature Ecology & Evolution

Toward Reducing Phylostratigraphic Errors and Biases

(2018) Bryan A Moyers et al.   Genome Biology and Evolution

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

(2018) Xing-Xing Shen et al.   CELL

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

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

(2018) Christopher E Laumer et al.   eLife

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads

(2017) Yi-Jyun Luo et al.   Nature Ecology & Evolution

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

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

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Phylostratigraphic Bias Creates Spurious Patterns of Genome Evolution

(2016) Bryan Moyers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Xenacoelomorpha is the sister group to Nephrozoa

(2016) Johanna Taylor Cannon et al.   NATURE

Standardized benchmarking in the quest for orthologs

(2016) Adrian M Altenhoff et al.   NATURE METHODS

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

DendroBLAST: Approximate Phylogenetic Trees in the Absence of Multiple Sequence Alignments

(2013) Steven Kelly et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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