README.md

tree_distance

A package to compute distances between phylogenetic trees.

Supported distances:

• Robinson-Foulds distance
• Weighted Robinson-Foulds distance
• Euclidean distance
• Geodesic distance

Installation

pip install tree_distance

Example

t1 = PhyloTree(b"(a:3,b:4,(c:5,((d:6,e:7):.2,f:8):.3):.4);", False) # rooted = False
t2 = PhyloTree(b"(a:3,b:4,(d:5,((c:6,e:7):.2,f:8):.3):.4);", False)
getRobinsonFouldsDistance(t1, t2, normalise=False) # 4.0
getRobinsonFouldsDistance(t1, t2, normalise=True) # 0.666...

Tests

To run the tests:

mkdir build
cd build
cmake ..
make
./tests