Q1 Explain the difference between the phylogenetic methods discussed in the class this week?
a. On performance
b. On implementation
c. On memory and cpu requirements
Q2 UPGMA is a distance method,
a. Explain the main steps of this method.
b. What would be the use cases for this method?
Q3 You run a Bayes approach with 500 sequences and find that you do not find any separation between the nodes?
a) What is an explanation for this observation?
b) What would a possible solution?
Q4. (You run a Maximum likelihood approach with 10 sequences of highly conserved hemoglobins and you find human sequences among rodent sequences and far from other primates.
a) What is the reason for this observation?
b) What action do you suggest as solution to this issue?
Q5. The UPGMA has an ultrametric characteristic?
a) What is the ultrametic condition?
b) Why is this a problem in practical settings?
c) What alternative could you use in leu of UPGMA
