Systematic benchmarking of omics computational tools
Computational omics methods packaged as software have become essential to modern
biological research. The increasing dependence of scientists on these powerful software …
biological research. The increasing dependence of scientists on these powerful software …
A practical guide to design and assess a phylogenomic study
J Lozano-Fernandez - Genome Biology and Evolution, 2022 - academic.oup.com
Over the last decade, molecular systematics has undergone a change of paradigm as high-
throughput sequencing now makes it possible to reconstruct evolutionary relationships …
throughput sequencing now makes it possible to reconstruct evolutionary relationships …
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation
Intrinsically disordered proteins and protein regions (IDPs/IDRs) exist without a single well-
defined conformation. They carry out important biological functions with multifaceted roles …
defined conformation. They carry out important biological functions with multifaceted roles …
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
Abstract eggNOG is a public database of orthology relationships, gene evolutionary histories
and functional annotations. Here, we present version 5.0, featuring a major update of the …
and functional annotations. Here, we present version 5.0, featuring a major update of the …
OrthoFinder: phylogenetic orthology inference for comparative genomics
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 …
high accuracy orthogroup inference to provide phylogenetic inference of orthologs, rooted …
UniProt: a worldwide hub of protein knowledge
UniProt Consortium - Nucleic acids research, 2019 - academic.oup.com
Abstract The UniProt Knowledgebase is a collection of sequences and annotations for over
120 million proteins across all branches of life. Detailed annotations extracted from the …
120 million proteins across all branches of life. Detailed annotations extracted from the …
OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species
L Xu, Z Dong, L Fang, Y Luo, Z Wei, H Guo… - Nucleic acids …, 2019 - academic.oup.com
OrthoVenn is a powerful web platform for the comparison and analysis of whole-genome
orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new …
orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new …
eggNOG 6.0: enabling comparative genomics across 12 535 organisms
The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database
is a bioinformatics resource providing orthology data and comprehensive functional …
is a bioinformatics resource providing orthology data and comprehensive functional …
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper
Orthology assignment is ideally suited for functional inference. However, because predicting
orthology is computationally intensive at large scale, and most pipelines are relatively …
orthology is computationally intensive at large scale, and most pipelines are relatively …
OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes
OrthoList, a compendium of Caenorhabditis elegans genes with human orthologs compiled
in 2011 by a meta-analysis of four orthology-prediction methods, has been a popular tool for …
in 2011 by a meta-analysis of four orthology-prediction methods, has been a popular tool for …