12 Introduction to Phylogenies.ppt

文档介绍：Building Phylogenies
ic (evolutionary) trees
Human
Gorilla
Chimp
Gibbon
Orangutan
Describe evolutionary relationships between species
Cannot be known with certainty!
Nevertheless, phylogenies can be useful
Human
Gorilla
Chimp
Gibbon
Orangutan
??
or
Applications of ic Analysis
Inferring function
Closely related sequences occupy neighboring branches of tree
Tracking changes in rapidly evolving populations (., viruses)
Which genes are under selection?
Phyloinformatics
Comparative analysis through phylogenies helps to understand biological function
Exploit phylogenies for data mining
Disease Transmission and Medical Forensics
Discovering Snake Antivenin
Methods
Distance-based
Parsimony
Maximum likelihood
Distance Matrices
a 0
b 6 0
c 7 3 0
d 14 10 9 0
a b c d
a
b
c
d
1
2
3
4
5
0
6
7
8
Ultrametric Matrices
a 0
b 2 0
c 6 6 0
d 10 10 10 0
a b c d
a
b
c
d
1
2
3
4
5
0
Least Squares
Dij = distance between i and j in matrix
dij = distance between i and j in tree
Objetive: Find tree that minimizes