CS 490/590 Bioinformatics Project V: UPGMA for Phylogenetic Trees
Description: You are to implement the UPGMA clustering algorithm on input sets of multi-aligned sequences to construct phylogenetic trees.
Specifications: Your input (as file sequences1.txt) will be a set of multiply-aligned DNA sequences, such as the alignment.fasta sequences of the previous project with added labels in each sequence’s header. As in the previous project, each sequence is a representative of its organism, and you will compute a distance matrix of those sequences based on the Jukes-Cantor distance calculations. You will run the centroid-linkage based UPGMA algorithm to cluster the organisms based on the distance metrics. Your final output, to the console, should be in the parentheses-based Newick format.
What to turn in: You must turn in a single zipped file containing your source code, a Makefile if needed for compilation, and a README file indicating how to execute your program.
Your program must be written in C/C++ or Java and compile using an open source compiler such as g++, gcc, or javac.
