Aleksandr Koshkarov
Project
Novel algorithms for comparing phylogenetic trees defined on different, but overlapping sets of taxaIn this study, we will develop new algorithms to compare phylogenetic trees with different, but overlapping leaves in the context of supertrees. A large community of scientists will highly benefit from our novel methods, including evolutionary and molecular biologists interested in building supertrees. Furthemore, this theoretical foundation of this problem will help to evaluate, adapt and improve a metric for comparing phylogenetic supertrees. The new metric will become an additional standard and will help researchers work more efficiently with clusters of phylogenetic trees and supertrees. The main goal of the research is to develop new algorithms for comparing phylogenetic trees defined on different, but mutually overlapping sets of taxa in the context of supertrees. This work proposes three projects to create a computational framework for comparing supertrees: (1) design a new approach to data generation of phylogenetic trees with different numbers of overlapping leaves, and establish the mathematical and algorithmic foundations of a new metric for phylogenetic trees defined on different, but mutually overlapping sets of taxa, (2) extend the Density-Based Spatial Clustering of Applications with Noise (DBSCAN) algorithm and incorporate the new distance metric for clustering phylogenetic trees with specified characteristics, and (3) evaluate our proposed metric and the extended DBSCAN clustering algorithm on real data (COVID-19). The developed algorithms will be of great significance to many evolutionary studies through their integration into the Open Tree of Life project and will thus contribute to our better understanding of species biodiversity. This highly integrative and multidisciplinary project fits into the broad category of comparative genomics, a field in which Canada is a leader. The possibility of developing an established and widely used metric of phylogenetic distances for supertrees would further strengthen the position of Canada in this field.
