What is the Phylogenetic Tree Generator?
Generate phylogenetic trees in your browser from a distance matrix, aligned FASTA sequences, or an existing Newick string. UPGMA clustering builds ultrametric trees from pairwise distances; p-distances are computed for DNA alignments. View an SVG cladogram, ASCII tree, and export Newick format. Free, private, and instant.
How to use the Phylogenetic Tree Generator
- Choose distance matrix, aligned sequences, or Newick input.
- Paste your data (tab-separated distances or FASTA alignment).
- Review the SVG cladogram and ASCII tree layout.
- Copy the Newick string for import into other tools.
- Inspect the distance matrix when built from sequences.
Common use cases
- Teaching UPGMA clustering in an evolution or bioinformatics class
- Quick cladogram from a small pairwise distance table
- Converting aligned FASTA snippets into a Newick tree
Frequently asked questions
- What algorithm is used?
- Distance-based input uses UPGMA (unweighted pair group method with arithmetic mean), a hierarchical clustering method that produces ultrametric trees.
- How are sequence distances calculated?
- The tool uses simple p-distance: the fraction of differing non-gap positions in an aligned sequence set.
- What is Newick format?
- Newick is a standard parenthesized text format for trees, e.g. ((A:0.1,B:0.1):0.05,C:0.2); Branch lengths follow colons.
- Can I import an existing tree?
- Yes. Paste a Newick string to visualize it without rebuilding from distances.
- Is my sequence data uploaded?
- No. All tree building runs locally in your browser.
