PCB 4674 Lecture Notes - Lecture 39: Distance Matrix, Phylogenetic Tree, Neighbor Joining
14 Apr 2018
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Document Summary
When making a phylogenetic tree, cluster taxa based on genetic distance. Outcome is a single number, distance, between pairs of sequences. When making a phylogenetic tree, it finds the most likely tree given specific model of molecular evolution. Calculates probability of observed data given a particular tree. Millions of trees are compared and highest likelihood is preferred. A character shared by a set of species but not present in their common ancestor. Most similar pairs are joined and new node is created. New matrix is calculated using the node instead of the pairs. This method is quick and easy, but inaccurate. Identifies the tree topology with the shortest possible branch lengths given the data. It creates a pseudoreplicate data sets, analyzes them, then sums the percent of trees that have the branch as a measure of support. A statistical method for estimating the strength of evidence that a particular branch in a phylogeny exists.
