Microbial communities often exhibit incredible taxonomic diversity, raising questions
regarding the mechanisms enabling species coexistence and the role of this diversity in …

Abstract The Transporter Classification Database (TCDB; http://www. tcdb. org) is a freely
accessible reference database for transport protein research, which provides structural …

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 …

The intensive use of antibiotics results in their continuous release into the environment and
the subsequent widespread occurrence of antibiotic resistant bacteria (ARB), antibiotic …

Abstract eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at
different taxonomic levels, each with integrated and summarized functional annotations …

Identifying homology relationships between sequences is fundamental to biological
research. Here we provide a novel orthogroup inference algorithm called OrthoFinder that …

The many functional partnerships and interactions that occur between proteins are at the
core of cellular processing and their systematic characterization helps to provide context in …

Genome-scale human protein–protein interaction networks are critical to understanding cell
biology and interpreting genomic data, but challenging to produce experimentally. Through …

Microbial genome sequencing projects produce numerous sequences of deduced proteins,
only a small fraction of which have been or will ever be studied experimentally. This leaves …

Abstract SMART (Simple Modular Architecture Research Tool) is a web resource
(http://smart. embl. de/) providing simple identification and extensive annotation of protein …