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Treemble Use Cases

Treemble is a lightweight, canvas-based tool for extracting, editing, and exporting tree topologies in Newick (and SVG) form. While it’s built with phylogenetic researchers in mind, its flexible canvas and Newick import/export make it valuable for anyone working with hierarchical or tree-structured data.

1. Biology & Phylogenetics​

  • Reanalyze published trees
    Import a PNG/PDF from a paper, extract the Newick, and run your own downstream analyses (e.g., dating, model tests).

  • Combine or compare multiple topologies
    Merge clades from different studies into a single “supertree,” or rapidly sketch alternative hypotheses for topology testing.

  • Whiteboard→Analysis workflow
    Snap a photo of a rough draft on a whiteboard or paper, extract its Newick, then feed it directly into R, Python, or open it in MEGA, FigTree, or other phylogenetics software.

  • Interactive hypothesis generation
    Quickly sketch variations on a backbone tree to explore how different topologies affect downstream statistics.

  • Teaching phylogenetics / clustering
    Let students sketch trees by hand or drag-and-drop tip names, then immediately export a Newick string to see how their trees parse in R or Python, or open it in a tree editor like MEGA.

  • Dichotomous taxonomic keys
    Classic identification keys successively split specimens into two mutually exclusive groups at each step.

2. Dendrograms & Hierarchical Clustering​

  • Data science & machine learning
    Visualize and refine hierarchical clustering outputs (e.g. customer segments, gene expression clusters) by editing cluster shapes, pruning branches, or relabeling tips.

  • Decision-tree model diagrams
    Most machine-learning decision trees split on a yes/no criterion at every node, producing a binary tree.

3. Other Fields​

Treemble may be useful in many fields where Trees are used to represent hierarchical relationships.

  • Evolutionary trees in other settings Fields like linguistics also use evolutionary trees to represent ancestral splitting events through time.

  • Medical differential diagnosis trees
    Construct or refine yes/no diagnostic trees that help clinicians narrow possible conditions step-by-step.

  • Troubleshooting flowcharts (yes/no)
    Technical support or diagnostic guides that follow binary questions map cleanly onto bifurcating trees.

  • Choose-your-own-adventure narratives
    Story paths designed with two options at each decision point can be extracted and re-edited as binary trees.

  • Single-elimination tournament brackets
    Sports or e-sports brackets progress via head-to-head matches.

4. Figures, Posters & Publications​

  • Rapid figure prototyping
    Sketch a draft tree, export SVG, drop into Illustrator or Inkscape, and add styling—all in minutes instead of hours.

  • High-quality outputs
    Generate publication-ready vector images without manually aligning shapes in a graphics program.

Got another idea?​

Treemble’s blank canvas, Newick import/export, and SVG vector output mean any tree-structured diagram can be created, cleaned up, and shared—across biology, data science, humanities, and beyond. If you’ve found a novel way to use it, let us know on GitHub Discussions!