thresholdLikelihood​.m

Computes likelihood of a phylogenetic tree under the Threshold model of Wright and Fisher.

Computes the likelihood of a phylogeny (specified using a Phytree object) from binary character data, according to the threshold model of Felsenstein: an unobserved liability is assumed to evolve according to a Brownian process operating down the branch - we only observe whether these liabilities are positive or negative at each of the tips.
We compute the likelihood using the quadrature + dynamic programming algorithm described in
Hiscott, G., Fox, C. Parry, M. and Bryant, D. Efficient recycled algorithms for quantitative trait models on
phylogenies. http://arxiv.org/abs/1512.00890