Compact graphical representation of phylogenetic data and metadata with GraPhlAn

被引：681

作者：

Asnicar, Francesco ^{[1
]}

Weingart, George ^{[2
]}

Tickle, Timothy L. ^{[3
]}

Huttenhower, Curtis ^{[2
,3
]}

Segata, Nicola ^{[1
]}

机构：

[1] Univ Trento, Ctr Integrat Biol CIBIO, Trento, Italy

[2] Harvard Univ, Sch Publ Hlth, Biostat Dept, Cambridge, MA 02138 USA

[3] Broad Inst MIT & Harvard, Cambridge, MA USA

来源：

PEERJ | 2015年 / 3卷

基金：

美国国家科学基金会;

关键词：

Phylogenetic visualization; Graphical representation; Phylogenomics; Metagenomics; INTERACTIVE TREE; F-TYPE; GENOME; ANNOTATION; EVOLUTION; BACTERIA; DISPLAY; KEGG; TOOL;

D O I：

10.7717/peerj.1029

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

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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