Compact graphical representation of phylogenetic data and metadata with GraPhlAn

PeerJ. 2015 Jun 18;3:e1029. doi: 10.7717/peerj.1029. eCollection 2015.

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.

Keywords: Graphical representation; Metagenomics; Phylogenetic visualization; Phylogenomics.

Grant support

This work has been supported by NIH R01HG005969, NSF CAREER DBI-1053486, and W911NF-11-1-0473 to C.H. and by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no PCIG13-GA-2013-618833, startup funds from the Centre for Integrative Biology (University of Trento), by MIUR “Futuro in Ricerca” E68C13000500001, by Terme di Comano, and by from Fondazione Caritro to N.S. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.