CPSC 536A Notes for 01 Feb 6



Parsimony problem

Small parsimony problem

Fitch's Algorithm



use Fitch's algorithm to generate the sets and total cost of 4 as shown.

If m > 1, then Fitch's algorithm can be applied independently to each site in the sequence, and the tree scores per site can be summed to get the total score.

Large parsimony problem

Branch and Bound method

Nearest Neighbour Interchange

Maximum Likelihood


relies on 2 independence assumptions:

Jukes-Cantor model

....more on this next day.