Neighbor-Joining Methods Start with star-like tree. Find neighbors sequentially to minimize total length of all branches C B C D Studier& Kepler 1988 Q12=(N-2)d12-d1-d2 Where any 2 sequences can be 1 and 2 Try all possible sequence combinations. Whichever combination of pairs gives the smallest Q1 is the final tree
Neighbor-Joining Methods Start with star-like tree. Find neighbors sequentially to minimize total length of all branches A B D C D Studier & Kepler 1988: Q12=(N-2)d12 - Σ d1i - Σ d2i Where any 2 sequences can be 1 and 2 Try all possible sequence combinations. Whichever combination of pairs gives the smallest Q12 is the final tree! B A C
Maximum likelihood A purely statistical method Probablilities for every nucleotide substitution in a set of aligned sequences is considered Calculation of probabilities is complex since ancestor is unknown Test all possible trees and calculate the aggregate probablility Tree with single highest aggregate probablity is the most likely to reflect the true phylogenetic tree VERY COMPUTATONALLY INTENSE
Maximum Likelihood • A purely statistical method. • Probablilities for every nucleotide substitution in a set of aligned sequences is considered. • Calculation of probabilities is complex since ancestor is unknown • Test all possible trees and calculate the aggregate probablility. • Tree with single highest aggregate probablilty is the most likely to reflect the true phylogenetic tree. VERY COMPUTATIONALLY INTENSE
Parsimony Parsimony: a derogatory term from the 1930s and 1940s To describe someone who was especially careful with Spending money Biologically: Attach preference to an evolutionary pathway That minimizes the number of mutational events since (1)Mutations are rare events, and (2) The more unlikely events a model postulates, the less likely the model is to be true Parsimony: a character-based method, NoT a distance-based method
Parsimony Parsimony: a derogatory term from the 1930s and 1940s To describe someone who was especially careful with Spending money. Biologically: Attach preference to an evolutionary pathway That minimizes the number of mutational events since (1) Mutations are rare events, and (2) The more unlikely events a model postulates, the less l likely the model is to be true. Parsimony: a character-based method, NOT a distance-based method