Part IV: Maximum likelihood methods 1. Go to a. b. C. d. e. f. https://evolution.genetics.washington.edu/phylip/programs.html What are the assumptions of DNAML? What does DNAMLK do? How is DNAMLK related to DNAML?

What are the assumptions of DNAMLK? What is PROTML? Why isn't DNAML suited to protein sequence data?/nWhy can the inclusion of the third base in a codon be misleading when constructing phylogenetic trees? h. What is the strategy taken by DNAML? i. How does Felstenstein recommend that you compensate for the dependence on the order of species inputs? j. What is "star decomposition?" 2. Use MEGA 10 to construct Maximum Likelihood and Maximum Parsimony Trees from your previous alignments. How do they compare to the other trees?