The Quick Compare page, which you can find under "Compare Analyses" in the left-hand navigation panel, gives you a side-by-side comparison of the organisms contained across a set of samples.
Choose the settings you want to explore that the top of the page, including which taxonomic rank you wish to display, whether to show reads or abundance estimates, and below which percent to group low taxa.
We will generate a plot with the chosen settings. This is an interactable plot. You can hover over a taxon for one sample, and it will highlight for all of the samples. You can also click in to view just the reads/abundances for a given taxon.
You can add or remove samples, scale and filter the data, and summarize the samples at different taxonomic rankings. Every comparison can also be exported as a spreadsheet or publication-quality image. The Shannon and Simpson alpha diversity statistics are also displayed below each analysis. Note that these are calculated at the selected taxonomic rank.
For more advanced options on comparing samples in One Codex, you can read more about Custom Plots and analysis notebooks.