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Goals of Phylogenetic Analysis

Explore different types of phylogenetic methods like character-based, parsimony, likelihood, and distance-based for analyzing ancestral relationships among species based on sequence alignments. Learn about models like JC, K2P, F81, HKY, and REV, and the General Time Reversible Model. Discover distance methods and how they aim to minimize scores to find optimal trees.

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Goals of Phylogenetic Analysis

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  1. Goals of Phylogenetic Analysis • Given a multiple sequence alignment, determine the ancestral relationships among the species. • We assume that residues in a column are homologous, and that all columns have the same history. Time Hu Ch Go Gi

  2. Types of Phylogenetic Methods • Character-based • Parsimony • Likelihood • Distance-based • Neighbor joining (NJ) • UPGMA Involve optimizing a criterion based on fit of the residues to the tree. Involve optimizing a criterion based on fit of a matrix of pairwise distances to the tree

  3. A A A B C C C B D D D B We usually estimate unrooted trees For 4 sequences, there are only 3 unique unrooted trees.

  4. A A A C B B C D B D D C Parsimony Methods A ACGA B ATGC C GTGC D GCAA Tree 1 Tree 2 1 2 3 4 Tot Tree 1 1 2 1 2 6 Tree 2 2 2 1 2 7 Tree 3 2 1 1 1 5 Tree 3

  5. B A G Likelihood Methods x is the collection of all parameters affecting the evolution of sequences A, B, and G. is the collection of all data (sequences A, B, and G).

  6. Modeling sequence change • Typically, the evolution of DNA sequences is modeled at the level of single sites. • JC: Jukes-Cantor (1969) • K2P: Kimura (1980) • F81: Felsenstein (1981) • HKY: Hasegawa et al. (1985) • REV: Tavaré (1986)

  7. General Time Reversible Model A C G T A C G T

  8. B A G Under this assumption, the likelihood simplifies to a product of individual site likelihoods: and (Nucleotide in Species A, site k) x

  9. Distance Methods A B C D A 0 B .5 0 C .75 .25 0 D .5 1.0 .75 0 A ACGA B ATGC C GTGC D GCAA

  10. A C B D a c e b d Many distance methods seek to find the tree that minimizes a score such as:

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