Journal
PEERJ
Volume 3, Issue -, Pages -Publisher
PEERJ INC
DOI: 10.7717/peerj.1029
Keywords
Phylogenetic visualization; Graphical representation; Phylogenomics; Metagenomics
Categories
Funding
- NIH [R01HG005969]
- NSF CAREER [DBI-1053486, W911NF-11-1-0473]
- People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7) under REA grant [PCIG13-GA-2013-618833]
- Centre for Integrative Biology (University of Trento)
- MIUR Futuro in Ricerca [E68C13000500001]
- Terme di Comano
- Fondazione Caritro
- Div Of Biological Infrastructure
- Direct For Biological Sciences [1053486] Funding Source: National Science Foundation
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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.
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