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Beta diversity calculator (Jaccard / Bray–Curtis): compare samples

Compute between-sample differences (beta diversity) as a distance matrix using Jaccard (presence/absence) or Bray–Curtis (abundance). Paste an OTU/ASV table or import CSV, then explore results with a heatmap and PCoA (2D).

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How to use (3 steps)

  1. Choose an example, or paste an OTU/ASV table (or import a CSV/TSV file).
  2. Select a metric (Jaccard / Bray–Curtis) and preprocessing (relative abundance, etc.).
  3. Review the distance matrix, heatmap, and PCoA (export CSV/PNG if needed).

Beta diversity is useful for exploration and visualization, but statistical conclusions require additional analyses (tests or modeling).

Inputs

Metric & preprocessing

If sample depths differ, try “Relative abundance”.

Sample groups (optional: color points in PCoA)

Two columns: sample, group (header is optional).

Results

This tool is for exploration and learning. It does not claim statistical significance.

Share & export

The share URL restores settings only (input data is not included). To save inputs too, use JSON export.

Distance matrix

Heatmap

PCoA (2D)

Jaccard vs Bray–Curtis

Bray–Curtis can be affected by library size (sample depth). If needed, compare both counts and relative abundance.

Equations (reference)
  • Jaccard distance: d = 1 - |A∩B| / |A∪B|
  • Bray–Curtis dissimilarity: d = Σ|xᵢ - yᵢ| / Σ(xᵢ + yᵢ)

Here, A and B are sets of observed features, and xᵢ/yᵢ are feature values (relative abundance or counts). Axis directions are arbitrary, so flipping the PCoA plot does not change the meaning.

How to use this calculator effectively

This guide helps you use Beta diversity calculator (Jaccard / Bray–Curtis): compare samples in a repeatable way: define a baseline, change one variable at a time, and interpret outputs with explicit assumptions before you share or act on results.

How it works

The page applies deterministic logic to your inputs and shows rounded output for readability. Treat it as a comparison workflow: run one baseline case, adjust a single parameter, and measure both absolute and percentage deltas. If a result seems off, verify units, time basis, and sign conventions before drawing conclusions. This approach keeps your analysis reproducible across teammates and sessions.

When to use

Use this page when you need a fast estimate, a classroom check, or a practical what-if comparison. It works best for planning and prioritization steps where you need direction and magnitude quickly before investing in deeper modeling, manual spreadsheets, or formal external review.

Common mistakes to avoid

Interpretation and worked example

Run a baseline scenario and keep that result visible. Next, modify one assumption to reflect your realistic alternative and compare direction plus size of change. If the direction matches your domain expectation and the size is plausible, your setup is usually coherent. If not, check hidden defaults, boundary conditions, and interpretation notes before deciding which scenario to adopt.

See also

FAQ

What is beta diversity?

A way to describe how different samples are from each other as a distance (dissimilarity). Smaller means more similar; larger means more different.

What is the difference between Jaccard and Bray–Curtis?

Jaccard compares presence/absence only. Bray–Curtis also uses abundances (counts or relative abundance).

What is PCoA?

A method that places samples in 2D based on the distance matrix (principal coordinates analysis). Axis direction is arbitrary, so flipping does not change the meaning.

Can I claim statistical significance from this result alone?

No. Beta diversity is useful for exploration and visualization, but statistical testing requires additional analyses.

What should I do first on this page?

Start with the minimum required inputs or the first action shown near the primary button. Keep optional settings at defaults for a baseline run, then change one setting at a time so you can explain what caused each output change.

How to use Beta diversity calculator (Jaccard / Bray–Curtis): compare samples effectively

What this calculator does

This page is for estimating outcomes by changing inputs in one controlled workflow. The model keeps your focus on variables, not output shape. Start with stable assumptions, then test sensitivity by changing one key input at a time to observe directional impact.

Input meaning and unit policy

Each input has an expected unit and a typical range. For reliable interpretation, check whether you are using the same unit system, period, and base assumptions across all runs. Unit mismatch is the most common source of unexpected drift in numeric results.

Use-case sequence

A practical sequence is: first run with defaults, then create a baseline log, then run one alternative scenario, and finally compare only the changed output metric. This sequence reduces cognitive load and prevents false pattern recognition in early experiments.

Common mistakes to avoid

Avoid changing too many variables at once, mixing incompatible data sources, and interpreting a one-time output without checking robustness. A single contradictory input can flip conclusions, so keep each experiment minimal and document assumptions as part of your note.

Interpretation guidance

Review both magnitude and direction. Direction tells you whether a strategy moves outcomes in the desired direction, while magnitude helps you judge practicality. If both agree, you can proceed; if not, rebuild the baseline and verify constraints before deciding.

Comments

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