Estimating Phylogenetic Trees
Overview
Darwin: “Origin of the species”
PPT Slide
Tree
Node degrees
Rooted/unrooted Tree
Taxonomic Unit
Bifurcating tree
Estimate tree
Brute force impossible
Tree Building Methods
Distance based
Agglomerative Clustering Method
UPGMA
WPGMA
One problem with XPGMA
Neighbour Joining (NJ)
NJ vs UPGMA
Minimum Evolution
Character based methods
Statistical Testing: Bootstrapping
Example result
Practical use
Example
Clustal X guide tree
Resulting alignment
NJ tree from alignment
The two together
Programs used
How to Build Good Trees
How to Build Good Gene Trees
Evolutionary Functional Prediction
Email: inge@ii.uib.no
Home Page: http://www.ii.uib.no/~inge