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Cell and Systems Biology
Ron Ammar

Lab 4: Phylogenetics - Summary • Phylogenetic trees can clearly illustrate relationships between sequences that are not apparent from analyses such as MSAs • Trees are helpful for developing hypotheses regarding gene or protein function for molecular and biochemical studies Anatomy of phylogenetic trees • The only way to determine the evolutionary distance between two sequences is how far back in time you have to go before finding a common ancestor • Order of letters written does not represent closeness o D is not the most closely related to A • Newick format: (((A, B), C), D) Distance-Based Methods • First generate a distance matrix by preforming a pairwise comparison between all sequences and calculating the genetic distance between each pair o Genetic distance is the number of mismatches between the sequences • Pairwise distance matrix then used to identify the two most closely related sequences which become the first two branches • Pairwise distance matrix is then remade. Two most similar sequences that were identified in the last step are represented by a single node in the tree • Processes is continued until table collapses to a s
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