Metagenome Data Exploration and Visualization Tools. Individual microbiome samples such as the ‘Sludge/Australian’ sample, can be examined using the ‘Microbiome Details’ page, which includes relevant microbiome information (1). The ‘Phylogenetic Distribution of Genes’ tool (2) displays the distribution of best BLAST hits of protein-coding genes in the microbiome as a histogram, with counts of genes that have best BLASTp hits to proteins of isolate genomes in each phylum or class with more than 90% identity, 60–90% identity and 30–60% identity. The distribution of genes for each phylum/class can be projected onto the families in that phylum/class such as Betaproteobacteria, and then further projected onto the species in that family such as Rhodocyclaceae. The genes in the sample can be viewed in the context of an individual reference isolate genome such as Dechloromonas aromatica, using the ‘Reference Genome Context Viewer’ (3), or using a ‘Protein Recruitment Plot’ (4). For each gene on ‘Reference Genome Context Viewer’ and ‘Protein Recruitment Plot’, locus tag and scaffold coordinates are provided locally (by placing the cursor over the gene), while additional information is available in the ‘Gene Details’ page, which is linked to each gene.

Abundance Profile Tools. The ‘Abundance Profile Viewer’ (1) provides an overview of the relative abundance of protein families (COGs and Pfams) and functional families (enzymes) across selected metagenomes, normalized for genome size or using z-score. Abundance of protein/functional families is displayed as a heat map (2), with each cell hyperlinked to the list of genes assigned to a particular family. A protein family can be saved in the ‘Function Cart’ by clicking its identifier such as COG0642 (3). For protein families in the ‘Function Cart’ a selective ‘Function Profile’ can be also computed (4). The ‘Abundance Comparison’ tool (5) takes into account the stochastic nature of metagenome datasets and tests whether the differences in abundance can be ascribed to chance variation or not. In addition to the gene count based abundance, the results provided by this tool include an assessment of statistical significance in terms of D-score (6) or P-value.