Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling

JP Bernot, CL Owen, JM Wolfe, K Meland… - Molecular biology …, 2023 - academic.oup.com
The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group
of animals on earth, containing over 80% of animal species and half of animal biomass. It …

OrthoFinder: phylogenetic orthology inference for comparative genomics

DM Emms, S Kelly - Genome biology, 2019 - Springer
Here, we present a major advance of the OrthoFinder method. This extends OrthoFinder's
high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted …

[PDF][PDF] OrthoFinder2: fast and accurate phylogenomic orthology analysis from gene sequences

DM Emms, S Kelly - BioRxiv, 2018 - scholar.archive.org
Ortholog inference has fundamental importance across the biological sciences,
underpinning phylogenetics, comparative genomics and prediction of gene function. We …

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more

AM Altenhoff, CM Train, KJ Gilbert… - Nucleic acids …, 2021 - academic.oup.com
OMA is an established resource to elucidate evolutionary relationships among genes from
currently 2326 genomes covering all domains of life. OMA provides pairwise and groupwise …

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy

DM Emms, S Kelly - Genome biology, 2015 - Springer
Identifying homology relationships between sequences is fundamental to biological
research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that …

Ensembl comparative genomics resources

J Herrero, M Muffato, K Beal, S Fitzgerald, L Gordon… - Database, 2016 - academic.oup.com
Evolution provides the unifying framework with which to understand biology. The coherent
investigation of genic and genomic data often requires comparative genomics analyses …

GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis

B Contreras-Moreira, P Vinuesa - Applied and environmental …, 2013 - Am Soc Microbiol
ABSTRACT GET_HOMOLOGUES is an open-source software package that builds on
popular orthology-calling approaches making highly customizable and detailed pangenome …

Genenames. org: the HGNC resources in 2015

KA Gray, B Yates, RL Seal, MW Wright… - Nucleic acids …, 2015 - academic.oup.com
Abstract The HUGO Gene Nomenclature Committee (HGNC) based at the European
Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. To …

Universal allosteric mechanism for Gα activation by GPCRs

T Flock, CNJ Ravarani, D Sun, AJ Venkatakrishnan… - Nature, 2015 - nature.com
G protein-coupled receptors (GPCRs) allosterically activate heterotrimeric G proteins and
trigger GDP release. Given that there are∼ 800 human GPCRs and 16 different Gα genes …

eggNOG v4. 0: nested orthology inference across 3686 organisms

S Powell, K Forslund, D Szklarczyk… - Nucleic acids …, 2014 - academic.oup.com
With the increasing availability of various 'omics data, high-quality orthology assignment is
crucial for evolutionary and functional genomics studies. We here present the fourth version …