This page contains the supplementary materials referenced in Chapter 4 of the thesis "Algebraic Geometry of Phylogenetic Models."

The file SecantDimension.mw can be run in Maple to implement the tropical secant dimensions approach for the secant ideals in Chapter 4. The file provides code to verify the lower bound on the dimension of the CFN secant ideal of the 6-leaf caterpillar tree discussed in Section 4.2. It also provides code to verify the lower bounds on the secant ideals of the Plucker tree ideals needed to establish the base cases in the proof of Lemma 4.3.10.

The file CFN_6leaf_Caterpillar_Secant.m2 can be run in Macaulay2 to carry out the computations described in Section 4.2 for the CFN secant ideal of the 6-leaf snowflake tree. This code verifies that the ideal is generated by equations of degree 5 or less and computes its dimension and Hilbert series.