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assignment3 - BSC5936-Fall 2005 Computational Evolutionary...

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BSC5936-Fall 2005 Computational Evolutionary Biology Assignment 3 – Exhaustive search (ES) and Branch and bound method (BS) Use the depth-first algorithm in the text from the handout of lecture 3 as a guide. Add the capability of doing a exhaustive search and the branch-and-bound-method to your program. this is perhaps the time to install some kind of minimal text-based user interface. Several possibilities work: Give a menu with choices: for example have a menu that allows to change between the different tree searching algorithms, Menu: T Tree search strategy: Exhaustive Change the tree search strategy [Exhaustive | Branch-and-bound | ...]? Allow the user to input commands on a console, for example like MrBayes or Paup: for example you could specify at the prompt: set search=exhaustive or help which might result in something like this: set Syntax: set <option> Options: search Syntax: search=<method> Methods: Exhaustive Searches all possible trees and returns the best or set of best trees
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