8 7 6 3 1 2 4 5ġ 2 3 4 5 Tree-building methods: UPGMA Step 4: Last cluster! This is your tree. 6 7 1 2 4 5ġ 2 3 4 5 Tree-building methods: UPGMA Step 4: Keep going. Find the next two proteins with the smallest pairwise distance. 6 1 2ġ 2 3 4 5 Tree-building methods: UPGMA Step 3: Do it again. Get ready to put the numbers 1-5 at the bottom of your new tree.ġ 2 3 4 5 Tree-building methods: UPGMA Step 2: Find the two proteins with the smallest pairwise distance. Find the leaf with 0 weight and remove the leafġ 2 3 4 5 Tree-building methods: UPGMA UPGMA is unweighted pair group method using arithmetic meanġ 2 3 4 5 Tree-building methods: UPGMA Step 1: compute the pairwise distances of all the proteins.Reduce length of every hanging edge by the same small amount δ, then distance matrix is reduced by 2δ.Find the nearest leaves – combine to the same parent.Given a weighted tree, with weights on edges representing evolutionary distances.Repeat two steps above until all species are connected.Recompute distances between all clusters.Join the closest two clusters to form a larger one.From distance matrix, use a clustering method.Use JC or other models to compute pair-wise evolutionary distances Jukes-Cantor (JC) Kimura 2P Kamura.Golbins are first proteins to be sequenced ĭistance-based tree Calculate the pairwise alignments if two sequences are related, put them next to each other on the treeĬharacter-based tree: identify positions that best describe how characters (amino acids) are derived from common ancestors.Parsimony analysis involves the search for the tree with the fewest amino acid (or nucleotide) changes that account for the observed differences between taxa. Character-based methods include maximum parsimony and maximum likelihood.Examples of distance-based algorithms are UPGMA and neighbor-joining. Distance-based methods involve a distance metric, such as the number of amino acid changes between the sequences, or a distance score.
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