Compact graphical representation of phylogenetic data and metadata with GraPhlAn

TLDR

The growing availability of genomic and metagenomic data creates challenges for visualizing large‑scale microbial and community datasets alongside rich metadata. This study introduces GraPhlAn, a computational tool designed to generate high‑quality, compact visualizations of microbial genomes and metagenomes. GraPhlAn is an open‑source, command‑driven application that supports phylogenies of thousands of taxa annotated with diverse metadata, and can be run locally or via a Galaxy web interface for seamless integration into bioinformatics pipelines. Illustrative examples of taxonomic, phylogenetic, metabolic, and biomarker visualizations demonstrate GraPhlAn’s utility for modern microbial and community genomics.

Abstract

The increased availability of genomic and metagenomic data poses challenges at multiple analysis levels, including visualization of very large-scale microbial and microbial community data paired with rich metadata. We developed GraPhlAn (Graphical Phylogenetic Analysis), a computational tool that produces high-quality, compact visualizations of microbial genomes and metagenomes. This includes phylogenies spanning up to thousands of taxa, annotated with metadata ranging from microbial community abundances to microbial physiology or host and environmental phenotypes. GraPhlAn has been developed as an open-source command-driven tool in order to be easily integrated into complex, publication-quality bioinformatics pipelines. It can be executed either locally or through an online Galaxy web application. We present several examples including taxonomic and phylogenetic visualization of microbial communities, metabolic functions, and biomarker discovery that illustrate GraPhlAn’s potential for modern microbial and community genomics.