Figure 4.

Comparing the phylogenetic composition of four metagenomes. Initially (a) the user selects a subset of metagenomes or genomes (here we selected 2 Soudan mine samples and 2 marine samples). The next step (b) allows selecting the basis for the comparison (protein-based-only SEED subsystems or all SEED proteins vs. RNA based RDP or Greengenes) and the parameters for the matches. The parameters include e-value, minimal alignment length, p-value, and percent identity. Finally, the result (c) is displayed in tabular format, in which a heatmap-style color coding is used to highlight differences. The resulting table can be downloaded as a spreadsheet.

Meyer et al. BMC Bioinformatics 2008 9:386   doi:10.1186/1471-2105-9-386
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