Free Dendrogram Maker for Hierarchical Clustering

Paste a header row, sample names in the first column and numeric features in the remaining columns. Dendrogram Maker accepts Excel cell paste, CSV, TSV or TXT. Select the features to compare, then choose a distance, scaling and linkage. For XLSX, paste its cells or save as CSV first.

All clustering, method comparisons, pair inspections, project files and SVG/PNG/CSV exports are free without an account, credits or watermark. Calculations run in your browser. Use up to 100 samples and 50 selected numeric features, or a full 100 × 100 distance matrix.

Each leaf represents a sample; each branch joins two existing clusters at a calculated height. In the classroom dendrogram clustering example, A=0 and B=1 merge at height 1 with single linkage. Read distance from the merge-height axis, rather than spacing between labels. Different linkage methods can produce different trees.

A dendrogram in clustering shows how samples join into nested groups. A cut at height h includes merges at h or below; connections above it stay separate. Move the cut line to inspect cluster members. Equal-height merges can change several groups at once. Visual separation does not establish statistical significance.

Choose Distance matrix and supply a full symmetric, nonnegative square matrix with zero diagonal entries. Row and column labels must match in the same order. Dendrogram Maker uses those supplied distances directly, bypassing metric selection and feature scaling. Triangular-only matrices are not accepted; resolve missing values before calculating.

Open Compare & inspect after generating a tree, then choose Compare 3 methods. The table compares single, complete and average linkage using the same input, distance and scaling. Cophenetic r measures linear agreement with input distances; it does not prove valid groups. Apply a method or download the comparison CSV.

Select two different samples in Compare & inspect. The inspector reports their input distance, first shared merge height, node ID, complete shared-cluster membership and relationship at your current cut. Highlight the shared subtree on the main diagram or download pair CSV; highlighting leaves the calculated tree and cluster membership unchanged.

Use Save project JSON to keep the source table, selected features, calculation settings, cut and layout. Restore files up to 1 MB to recalculate locally later; there is no automatic account storage. Export SVG or PNG and keep membership, merge or comparison CSV alongside it. Project files contain your source data.