Albert-Ludwigs-Universität Freiburg
Lehrstuhl für Bioinformatik - Institut für Informatik - http://www.bioinf.uni-freiburg.de
In this programming assignment we want you to implement functions that will allow you to generate a phylogenetic tree in Newick's format using an input distance matrix.
To this end, we provide helper classes Node, Tree and a function compute_distance to aid you in your task. Detail on how to use these helpers can be found in the exercise_sheet10.py file.
a) Implement the function convert_to_nodes which takes the distance matrix information and converts it to a list of nodes.
b) Implement the function merge_best_pair which takes a list of elements which can be both nodes and trees. It finds the best pair to merge based on the distance. Then it merges the two closest objects and returns a list with the merged object as well as the remaining unmerged ones.
Use the compute_distance function to determine the distance between two elements.
c) Implement the function build_the_tree which takes the distance information and outputs the final tree in Newick's representation.
Use your implementations of convert_to_nodes and merge_best_pair to create this function.