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TreeLogLikelihood

TreeLogLikelihood[SNPvec, tree, afreqvec, theta, epsilon, modelid]
returns the log likelihood for a single SNP data vector SNPvec given theta, espilon, the tree and the allele frequncy afreqvec at the SNP site.
TreeLogLikelihood[SNPmtx, trees, afreqmtx, theta, epsilon, modelid]
returns a list of log likelihood for multiple SNP data matrix SNPmtx given theta, espilon, the trees and the allele frequncies afreqmtx at SNP sites. Each row of SNPmtx corresponds data at a site.