Explicet is a visualization software application that facilitates analysis of taxonomy-based microbiome datasets. The goal of the Explicet development process was to create a powerful, yet intuitive, software tool for exploring and displaying complex microbiome datasets. Utilization of a graphical user interface (GUI) allows the user to concentrate on the science of a microbiome project, rather than the computational details.

Explicet is multi-platform and is currently provided for Mac OS X (10.6, 10.7, 10.8, 10.9), Windows (XP, Vista, 7, 8), and Linux (RHEL/CENTOS 5, 6). Explicet is fully compatible with taxonomically classified microbiome datasets produced by bundled tools such as Qiime [1], Mothur [10], and XplorSeq [4].

Explicet uses taxonomic classifications derived from DNA sequence data (e.g., rRNA gene sequences), combined with complete integration of project metadata, to produce tables and graphical plots (such as x-y charts, heatmaps, pie charts, and stacked bar charts) that portray the make-up of microbial communities from many perspectives. Explicet includes the ability to calculate and graphically display statistical metrics of alpha and beta diversity such as Sobs, Chao1, Good’s coverage, and Morisita-Horn. Additionally, Explicet includes several statistical computations (Two-Part, Two-Proportions, and Wilcoxon) that assess associations between the prevalence or abundance of taxonomic groups and a categorical variable (e.g., “healthy” and “sick”). Explicet provides data management capabilities that allow a dataset to be subdivided by metadata, sample name, and/or taxonomy. All tables and graphics generated by Explicet may be saved as named “figures” that can be recalled for modification and exported for publication.

Graphics output by Explicet may be in either bit-map formats (such as .png) or vector formats (.pdf), which are readily imported by tools such as Microsoft Word, PowerPoint, and Adobe Illustrator. Tables generated by Explicet are formatted as comma-separated-value files (.csv), which can be easily imported into Microsoft Excel, GraphPad, R, and SAS.

Although developed to facilitate the analysis of rRNA sequence data, Explicet can also be used to analyze other count-based datasets with hierarchical structure (e.g., metagenomic data, gene sequences other than rRNA).

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