🌳 Robinson-Foulds (RF) Distance

🔬 Definition

The Robinson-Foulds (RF) distance is a metric used to measure the topological difference between two phylogenetic trees.

It compares how trees partition the same set of taxa.

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🧠 Mathematical Formulation

Let:

• T1 and T2 be two trees
• S1 = set of splits in T1
• S2 = set of splits in T2

Then:

RF(T1, T2) = |S1 - S2| + |S2 - S1|

Equivalent form:

RF(T1, T2) = 2 × (number of non-common splits)

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🌳 Interpretation

• RF = 0 → trees are identical
• Low RF → trees are similar
• High RF → trees are very different

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📌 Example

Tree 1:

(A, B) | (C, D)

Tree 2:

(A, C) | (B, D)

👉 No common splits

RF = 2

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🧬 Biological Meaning

• Each split = evolutionary separation
• RF measures disagreement between evolutionary hypotheses

👉 Low RF:

• similar ancestry assumptions

👉 High RF:

• different evolutionary scenarios

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⚙️ Use in This Project

RF distance is used to:

• compute similarity between phylogenetic trees
• build a distance matrix
• serve as input for clustering

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