Input format

• Trees must be in Newick format.
• Example: (A:0.1,B:0.2,(C:0.3,D:0.4):0.5);
• Accepted extensions: .nwk .newick .new .txt .tree

Clustering modes

• Auto — Finds optimal k using the clustering validity index peak detection.
• Fixed k — Partitions the tree into exactly k clusters.
• Multi-resolution — Finds one optimal k per log-spaced bin.

How to use

1. Upload a Newick file or paste a tree string.
2. Select clustering mode and set parameters.
3. Click Run PhytClust (or press Ctrl+Enter).
4. Explore results in the tabs.
5. Use Export to download results.

Tree interaction

• Click internal nodes to collapse/expand subtrees.
• Right-click any node to rename, highlight, or resize.
• Scroll to zoom, drag to pan.
• Use the search box to find and highlight nodes by name.

Comparison mode

• Enable "Compute all clusters" to compare multiple k results from one run.
• Click Add comparison bar to add any number of cluster bars.
• Each bar can be sourced from computed k values or from a CSV/TSV file with two columns: leaf_name and cluster_id.
• You can set a custom title per comparison bar; this title appears above each bar in the plot.

Quick start

Load an example tree to see PhytClust in action:

Load example tree