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Suplementary Materials for "Combinatorial and computational investigations of Neighbor-Joining bias"

Suplementary Materials for:
"Combinatorial and computational investigations of Neighbor-Joining bias"



This page contains the Mathematica Notebooks associated with the paper Combinatorial and computational investigations of Neighbor-Joining bias by Ruth Davidson and Abraham Martín del Campo.

The notebook RegularNJ.m simulates the spherical fraction of the polyhedral subdivision of the Neighbor-Joining algorithm (without any bias correction in the last step).
The notebooks UniformNJ.m and BaggageNJ.m are variations of the notebook RegularNJ using either the Uniform or the Baggage bias corrections on the last step.

Data: We simulated 1,000,000 points taken uniformly from the intersection of the unit sphere and the possitive orthant to estimate the spherical fraction of the polyhedral regions defined by the NJ algorithm. We include our simulations for 4,5,6,7,and 8 taxa as well as the Mathematica notebooks in the file DataCodeNJcones.zip.