[SOLVED] CS490-590 Project 5- UPGMA for Phylogenetic Trees

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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.

  • JC-UPGMA-8bjppw.zip