What is the message length of a tuple?
S4: What is the message length of an alignment? S5: What is the message length of the strings given the tree, considering all alignments taken together? (R2) S5′: What is the message length of the strings given the tree and based on 1 optimal alignment? (R3) The answers to these sub-problems are not independent. The topology and parameter values define the tuple probabilities and thus the alignment probabilities and the plausibility of each tree. Two competing sets of answers to the sub-problems can be judged easily and objectively but finding the best answers is hard. On the other hand, algorithms for the sub-problems are largely independent and can be studied as such. A prototype program has been written for R3 based on one set of approaches to these problems. Some other possibilities have also been investigated. These are discussed below.
