Keep this page open in a separate browser window for quick reference.
Use the Dataset dropdown at the top of the page to choose a UMAP projection. Each dataset represents a different set of organisms and/or distance metric. Points load in chunks; a progress indicator appears while loading. Once loaded, each dot is one organism.
Two modes control what a mouse drag does on the plot:
Switch modes with the Select / Zoom buttons in the toolbar, or use Select Visible after zooming to grab all visible organisms at once.
Keep previous selections — when checked, a new box-drag adds to the existing selection rather than replacing it. Useful for combining two separate regions.
Drag on the plot in Select mode to draw a selection box. All organisms inside are highlighted and listed in the right panel.
Pinning lets you lock specific organisms into the active set so they survive a new box-drag that would otherwise replace your selection.
Each organism in the selection list has a small checkbox to its left. Checking it pins that organism — it will stay in the list (shown with a blue tint) even after you drag-select a new region.
The active set is always currently selected + pinned (duplicates removed). The count line reads N selected + M pinned when both are present. All analysis tools (Profiles, Trees, T-Test, Clusters) operate on the full active set.
The Show dots radio buttons (below the main toolbar) let you focus the plot by hiding irrelevant organisms:
The filter is persistent: it stays active as you drag new selections. Switching to Selected only gives you a live-focus view — as you drag, only the newly selected dots appear against an empty background.
The dot filter is automatically disabled (hidden) when Show Taxonomy is turned on, and restored when you turn it off.
Opens the protein family heatmap for a set of organisms (maximum 100). Two buttons:
Both buttons open the heatmap in a new browser tab, so you can keep the plot open.
These buttons appear in the lower toolbar when the active set meets the tool's size requirement. All tools open in a new tab and share a navigation bar so you can move between them.
| Tool | What it does | Size limit |
|---|---|---|
| View Profiles | Pfam / CAZyme family heatmap | 1 – 100 organisms |
| Make Trees | Neighbor-joining phylogenetic tree from profile distances | 2 – 200 organisms |
| T-Test | Welch's t-test: selected group vs. rest of dataset | 2 – 500 organisms |
| Find Clusters | DBSCAN clustering + per-cluster Pfam enrichment | 10+ organisms |
| Compare Regions | T-test between two user-drawn regions | 2 – 500 per region |
Check Show Taxonomy to recolor dots by taxonomic group instead of their default dataset colors. Use the adjacent dropdown to choose the rank (Auto, Domain, Kingdom, Phylum, Class, Order, Family, Genus).
Auto picks a rank that produces readable color groupings given the current selection.
Taxonomy coloring temporarily disables the Show dots filter. When you uncheck Show Taxonomy, the filter is restored and re-applied.
Type a name or partial taxonomy string in the left search box. Results are matched client-side against the loaded dataset — no extra network request. Selecting a result highlights that organism on the plot and adds it to the selection list.
Type in the right search box to search by Pfam ID, name, or description (server-side). Selecting a Pfam result colors all organisms on the plot by how many copies of that family they carry, using a threshold you can adjust with the Min count filter that appears.